biopipen 0.32.1__py3-none-any.whl → 0.33.0__py3-none-any.whl

{biopipen-0.32.1.dist-info → biopipen-0.33.0.dist-info}/RECORD

@@ -1,35 +1,35 @@
-biopipen/__init__.py,sha256=31GIxCk9aH78VuRzCVgISUIgmg2AZWeGccuxRLBiXe8,23
+biopipen/__init__.py,sha256=6K931DiWIOR94oP_7w9oZPyA0wEqkdgU1lkcLFyRTMU,23
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
-biopipen/core/config.toml,sha256=7IXvviRicZ2D1h6x3BVgbLJ96nsh-ikvZ0sVlQepqFE,1944
+biopipen/core/config.toml,sha256=lZV_vbYWk6uqm19ZWJcsZCcSNqAdIfN2fOfamzxZpg4,2148
 biopipen/core/defaults.py,sha256=yPeehPLk_OYCf71IgRVCWuQRxLAMixDF81Ium0HtPKI,344
-biopipen/core/filters.py,sha256=5bZsbpdW7DCxqiteRdb2gelmXvfqWPmPsFxrpHdWsoE,12987
+biopipen/core/filters.py,sha256=mh7f0uOTF7oH4D_c7tkZwBA-U6NXNq73GtTg0yKl8gI,15974
 biopipen/core/proc.py,sha256=60lUP3PcUAaKbDETo9N5PEIoeOYrLgcSmuytmrhcx8g,912
-biopipen/core/testing.py,sha256=lZ_R5ZbYPO2NPuLHdbzg6HbD_f4j8paVVbyeUqwg6FE,3411
+biopipen/core/testing.py,sha256=22yOfbhjcWJQfpZd_TX5XVyaaUpi2FO6g67h7RnBc2M,3544
 biopipen/ns/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biopipen/ns/bam.py,sha256=OtvzEadx-zpr98PoZoozbQszcQBvtFDMuAtuwH-3JUw,11394
+biopipen/ns/bam.py,sha256=EzYj5PjZEsPkaHJOGAS_STWnnw9P7aW0WBtAkBw7cx0,12596
 biopipen/ns/bed.py,sha256=EqpSa7Hx6GImvJNghtV4uDo2PnPXeUt1Yq9AFWJP9_8,8159
-biopipen/ns/cellranger.py,sha256=yPBoNzVSY74J7uyVucaob5lqZKKru5-hYSM4f4Nr2OY,5553
-biopipen/ns/cellranger_pipeline.py,sha256=EWkPJTujamNSMQoRnKfhUiIj6TkMfRmCSUbPfd8Tv8E,4011
+biopipen/ns/cellranger.py,sha256=rZKE3eHbxMrUzw3XJihAYOuq07OA6fmvbnJcwdHiLzs,5876
+biopipen/ns/cellranger_pipeline.py,sha256=IjCCGpr1HB3R4nRyBcAgWmF0HsLYmHd6nGMn2-wkWOM,4075
 biopipen/ns/cnv.py,sha256=ssQAHf2MB675avoXVRkYy0vGiqIpRpRExywjhbymmBI,7811
 biopipen/ns/cnvkit.py,sha256=5mA2Q8-YDs4g1HoxtpB_NWnyZYwEThNr3s3wlubLQrQ,31130
-biopipen/ns/cnvkit_pipeline.py,sha256=DZZljwvwVEI9sRUYBdxkOIT5-CIPLH1tag_OIU86aes,37094
-biopipen/ns/delim.py,sha256=fejsh4KW1TG5oMZzAC238LvQhBz7brXkfl3BHfnLK5M,5612
+biopipen/ns/cnvkit_pipeline.py,sha256=Nlg4VLHV3iGKwFaXtVOyC-j4foI6GOUFbw2SgPs1KvQ,37162
+biopipen/ns/delim.py,sha256=QfSDgd3RJUvzKNxX6YRpsA3XhnipPK7SGGQzLV73wo0,6283
 biopipen/ns/gene.py,sha256=rty-Bjcf87v2vyb9X4kRvfrQ6XQYXgN4f2ftFO0nWA8,3888
 biopipen/ns/gsea.py,sha256=EsNRAPYsagaV2KYgr4Jv0KCnZGqayM209v4yOGGTIOI,7423
 biopipen/ns/misc.py,sha256=qXcm0RdR6W-xpYGgQn3v7JBeYRWwVm5gtgSj2tdVxx4,2935
 biopipen/ns/plot.py,sha256=XzLq0A8qCIQRbxhPEdWhEfbRZ8g3e4KriVz0RP8enNY,18078
-biopipen/ns/protein.py,sha256=33pzM-gvBTw0jH60mvfqnriM6uw2zj3katZ82nC9owI,3309
+biopipen/ns/protein.py,sha256=YJtlKoHI2p5yHdxKeQnNtm5QrbxDGOq1UXOdt_7tlTs,6391
 biopipen/ns/regulatory.py,sha256=gJjGVpJrdv-rg2t5UjK4AGuvtLNymaNYNvoD8PhlbvE,15929
 biopipen/ns/rnaseq.py,sha256=bKAa6friFWof4yDTWZQahm1MS-lrdetO1GqDKdfxXYc,7708
-biopipen/ns/scrna.py,sha256=viIfqTH_0f7kSpHpKfrUf7HUr_w-V_oRYRj1TwuXYNs,120878
+biopipen/ns/scrna.py,sha256=bZjIppqwmFb7Sc3GLyed8jd0tsvybSBq80uanmzU9WE,127673
 biopipen/ns/scrna_metabolic_landscape.py,sha256=6AhaynGG3lNRi96N2tReVT46BJMuEwooSSd2irBoN80,28347
-biopipen/ns/snp.py,sha256=-Jx5Hsv_7KV7TqLU0nHCaPkMEN0CFdi4tNVlyq0rUZ4,27259
+biopipen/ns/snp.py,sha256=iXWrw7Lmhf4_ct57HGT7JGTClCXUD4sZ2FzOgsC2pTg,28123
 biopipen/ns/stats.py,sha256=DlPyK5Vsg6ZEkV9SDS3aAw21eXzvOHgqeZDkXPhg7go,20509
 biopipen/ns/tcgamaf.py,sha256=AFbUJIxiMSvsVY3RcHgjRFuMnNh2DG3Mr5slLNEyz6o,1455
-biopipen/ns/tcr.py,sha256=0PCF8iPZ629z6P3RHoAWEpMWmuDslomTGcMopjqvXmE,88304
-biopipen/ns/vcf.py,sha256=OYWuAWADba1xLwvHmIPwXYin_rUaAFQq7N38DQvoYzs,22746
-biopipen/ns/web.py,sha256=4itJzaju8VBARIyZjDeh5rsVKpafFq_whixnvL8sXes,5368
+biopipen/ns/tcr.py,sha256=UgPLur8hk3J57o03OKjWA0OiNiO3hX3Rgde_7WY04vM,96004
+biopipen/ns/vcf.py,sha256=zjOH2qiSJsHACLmBqV-Tew-mn-peZgvYLAWjTLh7uTI,23823
+biopipen/ns/web.py,sha256=8VY4Xsb8UrzS4IkGUX_84GQP1JG6NcTZrV7f9tA1tUI,5458
 biopipen/reports/bam/CNAClinic.svelte,sha256=D4IxQcgDCPQZMbXog-aZP5iJEQTK2N4i0C60e_iXyfs,213
 biopipen/reports/bam/CNVpytor.svelte,sha256=s03SlhbEPd8-_44Dy_cqE8FSErhUdqStLK39te5o7ZE,1364
 biopipen/reports/bam/ControlFREEC.svelte,sha256=OwN96RW0dN-gtQ1zWKbXYZCYkkrOC0RQmP3UG4x7zqU,837
@@ -53,8 +53,8 @@ biopipen/reports/scrna/MarkersFinder.svelte,sha256=77rD1psj0VJykPDhfwS-B8mubvaas
 biopipen/reports/scrna/MetaMarkers.svelte,sha256=iIFRKjvVYrM1AtDWqq8UfeS8q23R8FKg2yepKAw2KSE,508
 biopipen/reports/scrna/RadarPlots.svelte,sha256=g_fp9d3vdnzk-egXPhkhhfWXOeG569Rj8rYLRIKmlLc,396
 biopipen/reports/scrna/ScFGSEA.svelte,sha256=Gqt-XjqsB3XgdR3XukvphwyMExZpScwqgEo7AD-gK6g,491
-biopipen/reports/scrna/SeuratClusterStats.svelte,sha256=rTsoOCiVm7lEyBYgu2ZVcKNGi4g6PynYoOSx0DHdTHo,429
-biopipen/reports/scrna/SeuratMap2Ref.svelte,sha256=1g-FEmvR2YMn0OF66qESNBWmGdHQY3u8QuG4M-T7Y4E,659
+biopipen/reports/scrna/SeuratClusterStats.svelte,sha256=4yXMYpgGWYzcAdNhs7gaAAulkVrsC00UY1PHeKyXPlI,437
+biopipen/reports/scrna/SeuratMap2Ref.svelte,sha256=I3yU8U8Aepcksfwvo54dSAY5gxxgyEKbOX8XYlACq1M,1093
 biopipen/reports/scrna/SeuratPreparing.svelte,sha256=CCQ3qodjfoQeMZhSZp7irvSqBt10m7urzcWEOHsZa8M,365
 biopipen/reports/scrna/TopExpressingGenes.svelte,sha256=tt5_Vjym4coFT8Bvz0s6ZcCioTOIwCj83jdCGqPCmUw,491
 biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte,sha256=4M8V6jDv1_ZviTsRdoYNQixoTnKiD06oPHzVabUTq6k,978
@@ -67,6 +67,7 @@ biopipen/reports/snp/PlinkHWE.svelte,sha256=nes-NTwatoxvLoRBCg6jPp0fSg5kZZkVngUR
 biopipen/reports/snp/PlinkHet.svelte,sha256=hlSGx3qVETvZg6cd6vf27EtGeRzwD86I01kMLyIHEC4,545
 biopipen/reports/snp/PlinkIBD.svelte,sha256=s7nepF52Q4hKhRnIZDTFXqG7SIvhGy0NtfnTpexG0mE,507
 biopipen/reports/tcr/CDR3AAPhyschem.svelte,sha256=_r1pi_yTu_KjC02aegZ52IEQY8Mq0p3nqW_o9wOFWf8,1530
+biopipen/reports/tcr/ClonalStats.svelte,sha256=yxSzrEGYiq9pcAZRtSCuHB4KOq4A1I-sXJ73Wb4OEBQ,367
 biopipen/reports/tcr/CloneResidency.svelte,sha256=pzjkdGAhB7STxlXkTY5wnTT3plhkAPKMdGa6jwKuwoc,470
 biopipen/reports/tcr/Immunarch.svelte,sha256=jHOGUCWREaDNUf1_s6h9Kx_sp-y_dDRqY1rWrx0o0LM,433
 biopipen/reports/tcr/SampleDiversity.svelte,sha256=GrPUpQ6aJPtyQHoFL9ayG6knpW6yZznqwo0ZVZ2tMl4,5524
@@ -74,65 +75,69 @@ biopipen/reports/tcr/TCRClusterStats.svelte,sha256=YGK5_Vp85QmUJZO1ZGtg1IWBsh9o-
 biopipen/reports/tcr/TESSA.svelte,sha256=S1tG0HIU5569ybV0shuTz1CN0JcqFrFNB7M6JCiGhm0,1948
 biopipen/reports/tcr/VJUsage.svelte,sha256=c9G2-APGG0l-c6b32aFOimrP_QYD-oELBASN4VabXmk,426
 biopipen/reports/utils/gsea.liq,sha256=5uxNPyIr0xd7nrZePJlIsRyqCPx1uVWso7ehE1F-C4k,3556
-biopipen/reports/utils/misc.liq,sha256=HLK3mkWtIMQqBtM2IIRFUdKKTcY8cvBtyHJB9DbWBdw,1653
+biopipen/reports/utils/misc.liq,sha256=hj9x4-vqPmVu0ZqoYeHqxanAmHHAlAySZ76YP0vFMEk,2146
 biopipen/reports/vcf/TruvariBenchSummary.svelte,sha256=yew8HRN-YahBzX504Micah5BTnoL_PQzQfN_87TiuOA,577
 biopipen/reports/vcf/TruvariConsistency.svelte,sha256=BBvtxi1EPmGH7j5M5zMOcLEhKWZOlKoXp1lrQGAmz_0,647
-biopipen/scripts/bam/BamMerge.py,sha256=Gd5P8V-CSsTAA8ZrUxetR-I49GjJ3VJNjrqu7-EZwXQ,3642
-biopipen/scripts/bam/BamSampling.py,sha256=Pi6CXAbBFVRGh8-0WrkB-3v3oxinfahQk11H0IdBNmQ,2312
-biopipen/scripts/bam/BamSplitChroms.py,sha256=b7GS2I4X0dLOhlPg_r9-buoIHTWlq6zHI3Rox94LXR8,4893
-biopipen/scripts/bam/BamSubsetByBed.py,sha256=QpY6WDJfbO3k2FdMyfgstFKgTdtOc1beGoUF5FI5EAc,1027
+biopipen/scripts/bam/BamMerge.py,sha256=dCjROmURFNQYqkPaZy2FVrz6WFqZrMVJ2GU1WjXmkdI,3662
+biopipen/scripts/bam/BamSampling.py,sha256=OzR3bRak3mqMF_7gHVCmdP9IinBxdUh5Ei8zF74isrw,2337
+biopipen/scripts/bam/BamSort.py,sha256=vCFWR0asRDhFFbWm-nZJPi4lwfwNtsANa9DB4CjzyrY,5112
+biopipen/scripts/bam/BamSplitChroms.py,sha256=TFIiX9NnvcHzRuOIhqNMiRZ5Dc64X6P7WGj1qz5ihlU,4995
+biopipen/scripts/bam/BamSubsetByBed.py,sha256=98M-oynqCTR_4afRASfM6CSN3-JG2kRnl6P5PVR3zdc,1030
 biopipen/scripts/bam/CNAClinic.R,sha256=mQXwtShL54HZXGCPqgPKPrU74_6K_8PqtOtG0mgA-F0,5062
-biopipen/scripts/bam/CNVpytor.py,sha256=hOUli9BDMOoth0or-tjUYC1AP3yNOuxUS6G3Rhcg99s,18000
-biopipen/scripts/bam/ControlFREEC.py,sha256=oX6iWsos-CfiT_ViDBrKeMOOIVdCKWrB-_MqzLgEF9s,3267
-biopipen/scripts/bed/Bed2Vcf.py,sha256=u0mp_2Y4UtEA839zq9UENesH6Gyiwd4sZQW9wFnBVU0,5090
-biopipen/scripts/bed/BedConsensus.py,sha256=gfAxuIalvCEpS0tiOyAJGPYGgHN0L-hm0K37Iteh5yw,2386
-biopipen/scripts/bed/BedLiftOver.sh,sha256=Y4gBsz9w4zhE29UmWojO6F4PXMMMWC1uCzjrxa19eOs,256
-biopipen/scripts/bed/BedtoolsIntersect.py,sha256=sFyXPL3kG59xa5eJwHumcQLw3lfabOXsq2-k8IgIqt4,1722
-biopipen/scripts/bed/BedtoolsMakeWindows.py,sha256=Ip4U0ORXti65g7znZeHEbvw2PGlCxoEfeucZmw4wb1o,1428
-biopipen/scripts/bed/BedtoolsMerge.py,sha256=7mt307V_wWa_ME0VfuMsVX0HgEwfDcZtY_bDvOPjFiQ,368
-biopipen/scripts/cellranger/CellRangerCount.py,sha256=b9kkHPpq-bFh-3XCUdxdMKg3SsZmEzZFrG3dbtb4fX8,2875
-biopipen/scripts/cellranger/CellRangerSummary.R,sha256=mVOCIHngEpJIKVD3tMG5UWqS0OQGGjY6yx6ikRcqQU4,11067
-biopipen/scripts/cellranger/CellRangerVdj.py,sha256=ipGkPzkiVy5IpPrYKUK4zgEIvz-aMJOKbMEN-bMStFE,2200
+biopipen/scripts/bam/CNVpytor.py,sha256=HItxRw9vMTrB9ooOp88Syus4pY0jUZ8ZgcA2WKNqeAk,18055
+biopipen/scripts/bam/ControlFREEC.py,sha256=mopG1bnFjR412MEVdP5aoLhJrUTuxZuOUjzjYazMUPY,3337
+biopipen/scripts/bed/Bed2Vcf.py,sha256=CyFzfHSau2ntgPHo4nSaaeRZbaXpbBoW8YmPxxWJQlc,5128
+biopipen/scripts/bed/BedConsensus.py,sha256=dgWEWCBX2cnZhxzJCF3WD8_JqlDAyPIDZlJ0Qiws0VA,2449
+biopipen/scripts/bed/BedLiftOver.sh,sha256=gTIYN_KnNtPxKTjGdk4EYhwQ-kgPN5rO5YVvG6kxB0k,327
+biopipen/scripts/bed/BedtoolsIntersect.py,sha256=lFE2I8fgpjKCqOJM_qH5cs0l7dXv1c3w36eTXzujBj8,1736
+biopipen/scripts/bed/BedtoolsMakeWindows.py,sha256=HRYFwCOU_MzhmnwimhPH5jBnIftEXBdkpK5U9tCJ2Xw,1436
+biopipen/scripts/bed/BedtoolsMerge.py,sha256=d20obKLaJQALDNQ-Jz--OiL8klHGN44octkKx1ysJ04,381
+biopipen/scripts/cellranger/CellRangerCount.py,sha256=Te_tscWv_r2oTKPezN0zAkfuoQ3wwNqZC1IrsXjySYk,3307
+biopipen/scripts/cellranger/CellRangerSummary.R,sha256=eLcgU3b2HdK0AaKNz1-B14atptJTsJFpr2W-VYx1C18,10788
+biopipen/scripts/cellranger/CellRangerVdj.py,sha256=APatSSEjRdOYF2lF-kafJACtvR8l8UlvKJQDtn9Gk18,2287
 biopipen/scripts/cnv/AneuploidyScore.R,sha256=Bpm1cU7VkoinoKKzMuzqFntS8hjdd2IpBUjDiZyM7l4,9163
 biopipen/scripts/cnv/AneuploidyScoreSummary.R,sha256=dSnekzXetM8BDmZPhHOS8WwEeOfszPfqthq6TrZ3aPc,12452
 biopipen/scripts/cnv/TMADScore.R,sha256=IH07REfBO3QB2QNWuwGY6LgAUAOE0lsfP6W0bS67zGs,1530
 biopipen/scripts/cnv/TMADScoreSummary.R,sha256=w58LD5xHnLal9jv53nBUGpQ8eTkAyEk1leCVN2T_ZaM,7109
-biopipen/scripts/cnvkit/CNVkitAccess.py,sha256=UerX66utY8UdlI1mlSVD7E9O0ByLnHzt6G3Urb8mCWE,689
-biopipen/scripts/cnvkit/CNVkitAutobin.py,sha256=H5YcQ8f7Vs01Wad_oEQ9_AKBo5bKW856hAxShD75oDA,1656
-biopipen/scripts/cnvkit/CNVkitBatch.py,sha256=uzb300XLPRzV1BOOug6dAmupZ5FtQamFoYslVmbdTCA,3794
-biopipen/scripts/cnvkit/CNVkitCall.py,sha256=NyOnMjwT4w-ID9YtNks6fp6BIG7OzkGHmYphcXzAy_M,3544
-biopipen/scripts/cnvkit/CNVkitCoverage.py,sha256=hTXh77QmMWy12Ipphdabkai19D0ZfKd7XF5Soc-HSG8,823
-biopipen/scripts/cnvkit/CNVkitDiagram.py,sha256=tvHW6wAZ9YXKb6sbdvWEO_HPjLK4LOYxrcnPkV8iUoA,1889
-biopipen/scripts/cnvkit/CNVkitFix.py,sha256=nZ7_15ba4zgTRpyQfyGAdcx1kCWyNTyjfEkKYxQumJA,1087
-biopipen/scripts/cnvkit/CNVkitGuessBaits.py,sha256=lrNNa3-jH87WCmdVv8lRmS894xT_zNjFjWXmi1oSG4U,2216
-biopipen/scripts/cnvkit/CNVkitHeatmap.py,sha256=gtLSI2ipnB9amEM_hJtl73iM-0jGG_fvn1uPMIlFa-o,2485
-biopipen/scripts/cnvkit/CNVkitReference.py,sha256=dO5vzqlgfecYUNJ3I2TvBdL_zKEJyKl3mRcL14GLDGU,1402
-biopipen/scripts/cnvkit/CNVkitScatter.py,sha256=7DhTiXPHEHbdXn0VFcDOR-wTP6sks08N94KG7zjo_Is,2728
-biopipen/scripts/cnvkit/CNVkitSegment.py,sha256=q5iGAjY6-yIehPcJpi3hX6EuGre0YgWTPkG_d5LEV48,1629
-biopipen/scripts/cnvkit/guess_baits.py,sha256=7OCMtSMHIJWWZv9qEYVXnB0N4hU_JaGEesKdkr6tvJc,10586
+biopipen/scripts/cnvkit/CNVkitAccess.py,sha256=QWYPeXx9jaOg8ldKlAAtH6GS4X64FO4ajU1cfOAYS4s,762
+biopipen/scripts/cnvkit/CNVkitAutobin.py,sha256=GdpWg_7NQwENU8Q_I1Mm6hngeyLEGdBEQL6TcFrwwPg,1975
+biopipen/scripts/cnvkit/CNVkitBatch.py,sha256=3P7mcGDaqL4L6gO6oH6NOj46bCCCM6S9AqVYSJ50rF4,3828
+biopipen/scripts/cnvkit/CNVkitCall.py,sha256=YSdOzsatvQHSNQj6C0mZWHAlc2xkQQOns9D67OVyWEQ,3567
+biopipen/scripts/cnvkit/CNVkitCoverage.py,sha256=Vrc-NHh0VB1fnRwrZCZO17bJtFaRBWLNKqT6OCIq3Fg,841
+biopipen/scripts/cnvkit/CNVkitDiagram.py,sha256=-hPLuULays8-Uu0R1ZGgffNpcA64qckq_HeDXpmWkI0,1927
+biopipen/scripts/cnvkit/CNVkitFix.py,sha256=dBgPbRfN--3tVsPXCaD4kMR-MdeAfWVGYhjq3l5cljw,1106
+biopipen/scripts/cnvkit/CNVkitGuessBaits.py,sha256=hyHhaNI8YEEaAXd61FNYdBKnf0iLHds_Pg36M15ejFE,2357
+biopipen/scripts/cnvkit/CNVkitHeatmap.py,sha256=EYgqkga-OaiWO0Z7voBXQ0BSjZzeAxi8wSbcUvfwHtg,2517
+biopipen/scripts/cnvkit/CNVkitReference.py,sha256=DUnVp9R04iEK-YgQBKvai8s_SP3O0N6h6q0MmjPxc6w,1416
+biopipen/scripts/cnvkit/CNVkitScatter.py,sha256=jDbYlMMuedih8qhbC65cqrNsNflWXSnHzIcZKEjk_BE,2766
+biopipen/scripts/cnvkit/CNVkitSegment.py,sha256=YIgLo6ka8fBG1Ylb8pmbquwUl5B7SY42YlzZHgmp8y0,1656
+biopipen/scripts/cnvkit/guess_baits.py,sha256=mTy3AmyH5tkC_Mb_5IhQ_c0RssEGaCmoLPEVsW81yrY,10691
 biopipen/scripts/delim/RowsBinder.R,sha256=1QtRiPdUoxR8st1nxBMyVXgpcLfeF-iGsMYHz-66L2s,1465
-biopipen/scripts/delim/SampleInfo.R,sha256=xnpOGHGOMZeD_Ay7PBN9GkqW34sVkTufMIhbxKTw3wU,6727
+biopipen/scripts/delim/SampleInfo.R,sha256=EyvpLHCn2jpMKKw7MvMPZVSmkV7ZBp02q93ZQxg_RPU,4296
 biopipen/scripts/gene/GeneNameConversion.R,sha256=Jy2ykhCj9ClSdQUfdYavh2LaBm0nOIXY2kJKmpsqOlI,1818
 biopipen/scripts/gene/GenePromoters.R,sha256=0ukq3-wpN6uq_cyJlQvKDVvy0Dv8cI5Htd9t2xpkEyk,2021
 biopipen/scripts/gsea/Enrichr.R,sha256=gqN93oE3OeqW_TXZiE_gNH89_o_XFwnOWcHxhTUMvNs,724
 biopipen/scripts/gsea/FGSEA.R,sha256=KpZWM-oskitRaMBDoXQoxa3zcSjZnN-fosKrzEgX28c,1525
 biopipen/scripts/gsea/GSEA.R,sha256=Qo-QUY4B539Hm2FbsS2lsfgAxP_2FrhtPUN1Feq1Jmc,1125
 biopipen/scripts/gsea/PreRank.R,sha256=qrqaf_0ghgpaS3d9XbNVCZS7ZEbZaEoxNzTQ2zkVB_Y,1398
-biopipen/scripts/misc/Config2File.py,sha256=NUio0uOEuZtUBpuByDSItYu9Kwu5mosb4pdPq5-QAmE,440
+biopipen/scripts/misc/Config2File.py,sha256=Lir5dCXDV-_cpOoACaRqi7jMcwzpWCNkA71ZcNr66J4,459
 biopipen/scripts/misc/Shell.sh,sha256=Rg8_DOfDFeUjZ_1_EVm2lbzyMLqcEv9A3k6SsTcfZZ0,493
-biopipen/scripts/misc/Str2File.py,sha256=99oQNxChxChNJ9vmD77b48cu-r_P_heSpx7A5wi3qTE,212
+biopipen/scripts/misc/Str2File.py,sha256=QgVStsdTrdQRu7mEdgZHu1y97O8THYGdmByAhfOY-zs,231
 biopipen/scripts/plot/Heatmap.R,sha256=xD_X-0J3kVdKPctTUGeBFXxNgd6N6XbBfBb3giFePJU,2045
 biopipen/scripts/plot/Manhattan.R,sha256=7lJwCX1d0zUpJVhVcmQ35ZtQELzkaDNnBTNHHc3cxW0,4754
 biopipen/scripts/plot/QQPlot.R,sha256=Xil19FJ7jbsxo1yU7dBhhZo2_95Gz6gpTyuv9F0RDNM,4115
 biopipen/scripts/plot/ROC.R,sha256=cjmmYRQycYisqRmlkZE9nbmwfo-04wdJKVmlOsiEFAM,2451
 biopipen/scripts/plot/Scatter.R,sha256=fg4H5rgdr6IePTMAIysiElnZme0vCh1T0wrwH2Q9xkM,2840
 biopipen/scripts/plot/VennDiagram.R,sha256=Am9umSGr2QxZc2MIMGMBhpoEqta3qt_ItF-9_Y53SXE,704
-biopipen/scripts/protein/Prodigy.py,sha256=W56e51SkaWqthrkCSr2HUqhE9NfJQWZj4y0HXIqaYRA,4459
+biopipen/scripts/protein/MMCIF2PDB.py,sha256=jKefr6wQA0abNwhvvqO1uXLKjqt3mBWb5IWxJeDyzs4,1143
+biopipen/scripts/protein/PDB2Fasta.py,sha256=HVsoRRpieobuPwemCz30_N0rJ7T4aGFTQKZryijCbYg,1932
+biopipen/scripts/protein/Prodigy.py,sha256=elA62U7WJ89TGEKobvjjd3Refjzr61S69PiVO0qF6DE,4493
 biopipen/scripts/protein/ProdigySummary.R,sha256=1s3ofk6Kvs--GAAvzV8SdAyq5LrYozWtIlL32b6ZarE,3806
+biopipen/scripts/protein/RMSD.py,sha256=zE0g9QKWqqpC8lhGoQIF54VqDw37FaOUkvk0vtYf4-c,6250
 biopipen/scripts/regulatory/MotifAffinityTest.R,sha256=McAnbduE_6SMD_4RuftBemPdfJD9LeFYUYwqL3fzfjU,3047
 biopipen/scripts/regulatory/MotifAffinityTest_AtSNP.R,sha256=lzP3EtmpMucWviLDgXLeP_JvG4VADykBOl49CkftiR8,4366
 biopipen/scripts/regulatory/MotifAffinityTest_MotifBreakR.R,sha256=WpkPVNvWonmZqQ8khdDg2VHhda7ZHexvLFGRz4qgv88,3304
-biopipen/scripts/regulatory/MotifScan.py,sha256=WtSbs8z08oeTgzjr0LfIDmjbUdknAh1raa_QPQ_NCFg,5336
+biopipen/scripts/regulatory/MotifScan.py,sha256=mxhRWp6NBGEMpWJOpwqIvzkKlrgnRvJApyCU91svh8E,5399
 biopipen/scripts/regulatory/VariantMotifPlot.R,sha256=RNnBc0bboGfrJOPk5CsUbFRBMBvVX8zgGsrI5eybNyo,2874
 biopipen/scripts/regulatory/motifs-common.R,sha256=7deFrEzZKYzNhmYTsBqqb91CbIj2vtF7lRiPX0yGkO8,13277
 biopipen/scripts/rnaseq/Simulation-ESCO.R,sha256=68cEHDdJclX8P8Q7ey9yBOfK09M_kxlL6zgYXsEL2Rs,6378
@@ -141,7 +146,7 @@ biopipen/scripts/rnaseq/Simulation.R,sha256=PK9tZS88AcBPStcFalZlMU0KE0gSqFSQvhUo
 biopipen/scripts/rnaseq/UnitConversion.R,sha256=pr1uZuzjapZKwIupE-xtE2HW-OwdVCGBVaHQ_3ipIDw,11377
 biopipen/scripts/scrna/AnnData2Seurat.R,sha256=PohvXtUziu0_A_HL5HaOYG1wSVdLgMaV8yhzEKDQT84,2814
 biopipen/scripts/scrna/CCPlotR-patch.R,sha256=KpB8fwacBaWaUNjIidcLUkMShLjS4Gq9UY8LUgIITB0,8369
-biopipen/scripts/scrna/CellCellCommunication.py,sha256=1txufcxFsniB9UET_L2RA2qaQZfjidjUbUsese_hoGE,2899
+biopipen/scripts/scrna/CellCellCommunication.py,sha256=xOxCp2YyM8yHm06TSRCfZkw-vPXK_qrzVqtmHMsleZ8,4380
 biopipen/scripts/scrna/CellCellCommunicationPlots.R,sha256=KE-yy7TkMjPz4opfQgosr6NfMQQYeg4mgzfDod-RJrQ,6104
 biopipen/scripts/scrna/CellTypeAnnotation-celltypist.R,sha256=2lkIwtSw2A21RCUBdo3BVUdAwsLTIq65NDA-ZR1YWE0,9644
 biopipen/scripts/scrna/CellTypeAnnotation-common.R,sha256=s2exGdJ3WM8mDDeBXGUxuKO1DAGVgRiirHaJD0lPgDw,336
@@ -150,95 +155,97 @@ biopipen/scripts/scrna/CellTypeAnnotation-hitype.R,sha256=zol-IF0jd3DTzw9I1UVUMY
 biopipen/scripts/scrna/CellTypeAnnotation-sccatch.R,sha256=LTvFzGzP0nmQLkJIxn6H7L8xkP2Z3q52DknXtBkkmcA,1822
 biopipen/scripts/scrna/CellTypeAnnotation-sctype.R,sha256=RhFHy1E4b3Y7pw6feKEhPx5GTbNdaQMDXHzvRlPk34Q,4544
 biopipen/scripts/scrna/CellTypeAnnotation.R,sha256=X_LR0LZ6UQjLA-SCCcQ8CBFZGG_J8CUNx--qwBS8Oh8,773
-biopipen/scripts/scrna/CellsDistribution.R,sha256=QOkQhpendXMmgen99wn0Pl3XKnMJQzvLVb0hPdR49NQ,18980
+biopipen/scripts/scrna/CellsDistribution.R,sha256=Hq0EU6SLJtiMZQTy9Jb-MC1yMcWhcTdlhgr5qSKgP90,19717
 biopipen/scripts/scrna/DimPlots.R,sha256=oKhygoWQOCck8OlpnOrNJg0CS2q-r8Com1dfjTvQzvU,1575
 biopipen/scripts/scrna/ExprImputation-alra.R,sha256=xNdQiXgY13-iF16o2KgCJWfPIy4P-lOiO1bl9PfXI4U,864
 biopipen/scripts/scrna/ExprImputation-rmagic.R,sha256=jYIfqZpnvjKJkvItLnemPVtUApHBYQi1_L8rHVbEe1M,735
 biopipen/scripts/scrna/ExprImputation-scimpute.R,sha256=mg40qCUW7-nP5oHPvARq7dmtoahM0GRFWXQpum0BXVk,1082
 biopipen/scripts/scrna/ExprImputation.R,sha256=GcdZJpkDpq88hRQjtLZY5-byp8V43stEFm5T-pQbU6A,319
-biopipen/scripts/scrna/MarkersFinder.R,sha256=-PyxWYRX1t9VTJYJV7GpPmEIjq65Y8HHFCxy_jwId9g,23021
-biopipen/scripts/scrna/MetaMarkers.R,sha256=opw5RyHpNnYXXnw0HQvFSaptw3IDaTiArwT1EOj_zFg,12114
+biopipen/scripts/scrna/MarkersFinder.R,sha256=D3vhxVYAc6kgPLjw05_D5yaXOaYKHoiZ-4OvQ7RdZ6s,13297
+biopipen/scripts/scrna/MetaMarkers.R,sha256=gJexrokGg0Q53N4Y4UA6707mn9Jxv-g_Qpp4Pi6xrs8,12438
 biopipen/scripts/scrna/ModuleScoreCalculator.R,sha256=QJ_E6qjRC8GazoopcxZfT5cKxlubf4dK-V7KLBB-yRE,4210
-biopipen/scripts/scrna/RadarPlots.R,sha256=4zs0hAm7yq1Ls62f_29koPLqAKCeKbYiztNM-HR7j3U,13041
+biopipen/scripts/scrna/RadarPlots.R,sha256=ZNH7FAs8icNrxs64hazZ8RfvnAU4Rf64p00bfGjexH0,14529
 biopipen/scripts/scrna/SCImpute.R,sha256=dSJOHhmJ3x_72LBRXT72dbCti5oiB85CJ-OjWtqONbk,2958
+biopipen/scripts/scrna/SCP-plot.R,sha256=QcR2zOjRlSA_z4L8l89FWPU7TGxpXlKUe4kPdZU9MuY,787291
 biopipen/scripts/scrna/ScFGSEA.R,sha256=LxFxd46qGt2OlvpO-4YqcEiZhFoVdFpJ1AmhUdpaIUo,6323
 biopipen/scripts/scrna/ScSimulation.R,sha256=b2LtL68ucxLoI57tSEDD0hOSbVHUA_x88Y96eK07N-s,1712
+biopipen/scripts/scrna/ScVelo.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/scripts/scrna/Seurat2AnnData.R,sha256=zXkdHEqv6H8RCw1bEPStvYHVpu5oRnioWxz164MgHxQ,276
-biopipen/scripts/scrna/SeuratClusterStats-clustree.R,sha256=FkbniQMHiZGrFAIuS8nUfPVJKFofSL-ZnpxTqIhTa54,3058
-biopipen/scripts/scrna/SeuratClusterStats-dimplots.R,sha256=NEdlJHNXnJZfF7YkefYVWTPO8Z_KAppRAs9rNvB8TXs,2360
-biopipen/scripts/scrna/SeuratClusterStats-features.R,sha256=ae3hdEPzC3bO11ot2-xH6AT3-v8GWCxAxcm05xH4TBI,15609
-biopipen/scripts/scrna/SeuratClusterStats-hists.R,sha256=PXyDKww8HcloCU8r4IqRwRrm6Ly0cpmpvRcP30xxBa4,5038
-biopipen/scripts/scrna/SeuratClusterStats-ngenes.R,sha256=ihZLB27iEhgICKj-ZTnxTvRAYIgg9rzWr9Oyh1YmOYM,2160
-biopipen/scripts/scrna/SeuratClusterStats-stats.R,sha256=jufs99zxNyUaTCDiWzO0yt76ncc73Yn_SpPa5igbJyA,9120
-biopipen/scripts/scrna/SeuratClusterStats.R,sha256=fywRBVjaFIJBxdgsZxLXEheUZI4l5VUoNIcJnhPIdPQ,2193
+biopipen/scripts/scrna/SeuratClusterStats-clustree.R,sha256=dbwvVE_EaOR0cyKDtel9sYKWMyEILaq475SjEXo7_-4,2868
+biopipen/scripts/scrna/SeuratClusterStats-dimplots.R,sha256=tCf3BVoXroeGuMcix8BiB1CA7wUpirBow4T6P3HM02k,1541
+biopipen/scripts/scrna/SeuratClusterStats-features.R,sha256=MGZbcMSaXWt3qCgNnBgdJs5LUTtWPFPtfyyEuA29nQk,4818
+biopipen/scripts/scrna/SeuratClusterStats-ngenes.R,sha256=NM0-iUf0tXEEZTgZpYokrrRIYXN4jGAoZkjP3T6TJ1k,2663
+biopipen/scripts/scrna/SeuratClusterStats-stats.R,sha256=peG1i7Aru0kIiHvubBlQFKKIXJyUpOdIyMCsud193h4,2255
+biopipen/scripts/scrna/SeuratClusterStats.R,sha256=MYMbR4suSRTkJJDYrS-GCE_3DRTyu6a85F12cO6S1dQ,1863
 biopipen/scripts/scrna/SeuratClustering-common.R,sha256=JX4Cn2FC6GOcBqaVyGDD3MM5zGpm3TpKJlfo2oOQ4Uk,8195
 biopipen/scripts/scrna/SeuratClustering.R,sha256=0OKRBQ5rFuupK7c03_sSt2HMwMdMnCYFqTvkRXFKchs,1706
 biopipen/scripts/scrna/SeuratFilter.R,sha256=BrYK0MLdaTtQvInMaQsmOt7oH_hlks0M1zykkJtg2lM,509
 biopipen/scripts/scrna/SeuratLoading.R,sha256=ekWKnHIqtQb3kHVQiVymAHXXqiUxs6KKefjZKjaykmk,900
-biopipen/scripts/scrna/SeuratMap2Ref.R,sha256=MP6ttYv8bK5kzWNoP3DXEad06snotVOqCqdvBHsOasc,12776
+biopipen/scripts/scrna/SeuratMap2Ref.R,sha256=Q5ivD5drhbOWA71bU1XH2tPUbsrV0zrXQ5zBvuK-6oo,13153
 biopipen/scripts/scrna/SeuratMetadataMutater.R,sha256=PMwG0Xvl_EEVKkicfrIi4arEqpY948PkYLkb59kTAXI,1135
-biopipen/scripts/scrna/SeuratPreparing-common.R,sha256=zLZ8nhSJK7otrc8e-2FswGc45WRYTE6tdHzKZSFVV2s,16347
-biopipen/scripts/scrna/SeuratPreparing-doublet_detection.R,sha256=TNN2lfFjpnnO0rguMsG38JYCP1nFUhcPLJ1LqGj-Sc8,6674
-biopipen/scripts/scrna/SeuratPreparing.R,sha256=CZL6h3mLS5C34ooMa4GcwvSPn4l46Lx7-sRi9FmWvJI,3827
+biopipen/scripts/scrna/SeuratPreparing.R,sha256=uaPR5_xqDQi35d5mOIpldbZ_IDS3Oc7w00mVBuyB3cM,6197
 biopipen/scripts/scrna/SeuratSplit.R,sha256=vdK11V39_Uo_NaOh76QWCtxObGaEr5Ynxqq0hTiSvsU,754
 biopipen/scripts/scrna/SeuratSubClustering.R,sha256=3MymNPsGUSi2hKlzSxTwhFogOfvqDAagcDR_tMAyt0Y,7593
 biopipen/scripts/scrna/SeuratSubset.R,sha256=yVA11NVE2FSSw-DhxQcJRapns0tNNHdyDYi5epO6SKM,1776
 biopipen/scripts/scrna/SeuratTo10X.R,sha256=1mh1R0Qlo1iHVrpMLUXyLDOA92QKJ4GzTMURTFRqsWg,901
+biopipen/scripts/scrna/SlingShot.R,sha256=IMqbXlAVJNO5Y2vIT2kN4fgtDJDm355SMx_D6LUHi5s,1916
 biopipen/scripts/scrna/Subset10X.R,sha256=T2nJBTwOe12AIKC2FZsMSv6xx3s-67CYZokpz5wshqY,2679
-biopipen/scripts/scrna/TopExpressingGenes.R,sha256=gYoPjHlhypCmqbED8hYdrt4DKAGkHgSs_TqVzyvVUIQ,7496
-biopipen/scripts/scrna/celltypist-wrapper.py,sha256=f5M8f4rU5nC7l17RS0YVmUPpLLz4D6PIcgWtA77UExM,1722
+biopipen/scripts/scrna/TopExpressingGenes.R,sha256=0cE12HMrW_fJxxIqdVMnDbTo3J9M2VmjszJIZxfh0Qc,7676
+biopipen/scripts/scrna/celltypist-wrapper.py,sha256=LW3cVZQSdLrqUUuW-CrMS9ka6YSEozVMwf3YtmG08Fs,1765
 biopipen/scripts/scrna/sctype.R,sha256=NaUJkABwF5G1UVm1CCtcMbwLSj94Mo24mbYCKFqo1Bw,6524
 biopipen/scripts/scrna_metabolic_landscape/MetabolicFeatures.R,sha256=FN-nIRquw1pgQRviVx3us8ZdigugEjpjq22zIGSCoO4,5264
 biopipen/scripts/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.R,sha256=Qt2lc-z91A12rxtGtcpM3gKaxXR1xb8innSiCVV_Il0,5544
 biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayActivity.R,sha256=HwCjNupjF8pudBRjpOVZyfCxVCIprHYW2KNiMNbuP_w,16279
 biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.R,sha256=92Q-KCD8fvxpovrSDr6FUFlS5acsdad8RdmIWvqZZ3s,9894
 biopipen/scripts/snp/MatrixEQTL.R,sha256=nLM3E7Y3XTATcWV0e4c1GSoJc4xFKV49WeNLBTHjf9c,7223
-biopipen/scripts/snp/Plink2GTMat.py,sha256=ypxuT6YEBuuSk9TML9SHhVtA38GlZvB-3tQakJd8YLQ,5052
+biopipen/scripts/snp/Plink2GTMat.py,sha256=pqFxZgJJ0qcdb3alU8tglsFmBZPNPEXeRWOxrKp790Y,5583
 biopipen/scripts/snp/PlinkCallRate.R,sha256=ATieZsVIhBfs1cOgLnJ-Qwl2f2F9wfaVYQOjsozoRFk,6202
-biopipen/scripts/snp/PlinkFilter.py,sha256=eqC18ne3rPUzIJ_KjqvwQ79MyeMxe0oh4S9PnhfhK1E,3200
+biopipen/scripts/snp/PlinkFilter.py,sha256=I87x0o3VpTtqCu8y9HY1BLMBdESHfb5G-hSWykDUnvk,3250
 biopipen/scripts/snp/PlinkFreq.R,sha256=4HJRlu4j_hrdY6taXyCSt0ODrX47T2HjLFf4ZSnD2dU,10647
-biopipen/scripts/snp/PlinkFromVcf.py,sha256=TZaJ117Qp-gbqPX7WK6r7Zw8XHVXbRO6wb0V1NQouxw,2284
+biopipen/scripts/snp/PlinkFromVcf.py,sha256=uwXXWVCbdypdE3kcFo5h6c11mmNBttRxdHtycRiqgBo,2401
 biopipen/scripts/snp/PlinkHWE.R,sha256=QpGVDEkNNPvdJOWsB_ouBagNLv3W-ZQ34ur62bb-H1o,2243
 biopipen/scripts/snp/PlinkHet.R,sha256=eqDrRYX2NhsqBcm2Wp0kGKUtTNLtBHXVcLeJMP3QCns,3047
 biopipen/scripts/snp/PlinkIBD.R,sha256=hWW9emQmsS7jxA-J7-WZeAWrJPGl98YneNx-VU4qAuE,5754
-biopipen/scripts/snp/PlinkSimulation.py,sha256=mSSoGGG6sbEPBcUGdHgbebUrg4DiHeyNyc7jLPjV5pY,4169
-biopipen/scripts/snp/PlinkUpdateName.py,sha256=sYyb0ek46wRQfclFfoJEhQyQ-zWsFd2xpFHKw3jbsq4,4055
-biopipen/scripts/stats/ChowTest.R,sha256=TmoDbFJfEFsd0ZKwMdqTJI0dacxvrtHkJ1FP6FhJpcM,3638
+biopipen/scripts/snp/PlinkSimulation.py,sha256=OMnzp0OZdt7hQQoMbNa9nv-6NzH2x9-YI2FNX5IGaEQ,4193
+biopipen/scripts/snp/PlinkUpdateName.py,sha256=OTiI-oQT-e6f3WZaO98bnddzms2VUzWfMpGPJlg6O-c,4078
+biopipen/scripts/stats/ChowTest.R,sha256=jY1xD_YtwOUIv8K-LYr7BtZsLKVs0B-jJJjrfjBChmI,4489
 biopipen/scripts/stats/DiffCoexpr.R,sha256=kxiks9lRs5ssGfj1LdS3jetM_ILLVOXdiTjML6_0mHM,4537
 biopipen/scripts/stats/LiquidAssoc.R,sha256=EBwIl7xf83hlqYs_h9wcdjGLjbmJwmMiR5FM0QGgZfk,3748
 biopipen/scripts/stats/Mediation.R,sha256=3WFeltdENvx0v8P6m7DZbhuCSCMnBKE7B14e8ZLVYdU,3291
 biopipen/scripts/stats/MetaPvalue.R,sha256=s1ewfMwwcSSihsvungyUhSiJF-PDet0wXenAHFJfdTI,4139
 biopipen/scripts/stats/MetaPvalue1.R,sha256=Yearem_XmMaHfZbN_qmDSTNlvVddTSC5Z59zjVe_sno,1848
-biopipen/scripts/tcgamaf/Maf2Vcf.py,sha256=Cxh7fiSNCxWDTfIJqZDOOnaSrw-85S_fH2U-PWY03hc,704
-biopipen/scripts/tcgamaf/MafAddChr.py,sha256=V10HMisl12O3ZfXuRmFNdy5p-3mr43WCvy0GHxSpwfA,494
+biopipen/scripts/tcgamaf/Maf2Vcf.py,sha256=2MHraQRO2PuiywFpBTpaQMOT7Fc4GhsHfCAJ79A3Q3w,723
+biopipen/scripts/tcgamaf/MafAddChr.py,sha256=uo1utaK3Df88aU7xubKw85Ni7W06md8bQlwUh9oblew,512
 biopipen/scripts/tcgamaf/maf2vcf.pl,sha256=hJKcH-NbgWK6fmK7f3qex7ozJJl-PqCNPXqpwfcHwJg,22707
 biopipen/scripts/tcr/Attach2Seurat.R,sha256=0KZaBkuPvqOBXq4ZG3pzIIua5HL-161K5dVXRoCysy4,1366
-biopipen/scripts/tcr/CDR3AAPhyschem.R,sha256=ZxHyn4vJF-1PDbnbozovOipET_QZKqeFrKUibRpLgzw,16825
-biopipen/scripts/tcr/CloneResidency.R,sha256=KAcFB39vTYsk8IEj44s8oSFVhKjpAdJ8hkpKxtdWzRA,21540
+biopipen/scripts/tcr/CDR3AAPhyschem.R,sha256=fwMNMeBfJ437P3G9tQkVD52dnKyvPcI-4hyBncYQxeI,17161
+biopipen/scripts/tcr/ClonalStats.R,sha256=tvSgIFKRK4hYPeOm2scDRPktDH0hVV9qCYDw-lirLWo,29325
+biopipen/scripts/tcr/CloneResidency.R,sha256=RbQT81wVsh8N6YTT4BrAl6dbcQG7obDqI9-fEq_fYwk,22033
 biopipen/scripts/tcr/CloneSizeQQPlot.R,sha256=hds1C80Q_W40Ikp-BrFfvh_aBf_V61lz-1YAvkDESyk,4569
 biopipen/scripts/tcr/GIANA/GIANA.py,sha256=jo0d58K57CF4W6mc2Q-hQn9rLl6oLHTsr5JceP8xqN0,54874
 biopipen/scripts/tcr/GIANA/GIANA4.py,sha256=X_iXdgKZ9V5T87jXBdml0H6bwiDjsAqoPKhsdF72lj8,53904
 biopipen/scripts/tcr/GIANA/Imgt_Human_TRBV.fasta,sha256=XUwDPXJxVH5O9Q0gCL6EILKXEwVyiAZXm4VS2vkPcnQ,15371
 biopipen/scripts/tcr/GIANA/query.py,sha256=YJeCk24Hab7XfQxZ5VNesdjr_LVxPH0KH9rwGm1ePf4,7680
-biopipen/scripts/tcr/Immunarch-basic.R,sha256=2UAQtGEDKgf5LmPeGlNkkAfQOCtdYpCiBMAn-JHOV4A,3036
-biopipen/scripts/tcr/Immunarch-clonality.R,sha256=NN6WikD-9BKodgKRAbvM2oMLrhn9FUWjqIb69DpHnAk,3744
-biopipen/scripts/tcr/Immunarch-diversity.R,sha256=6T8-IXIMyy4YXgIA4TXJThy91FqgLVsljqxd3PxLDys,27136
-biopipen/scripts/tcr/Immunarch-geneusage.R,sha256=jcuZPxQq19Ics73OT58oGl34jSRghJAgT2JY-L99UgE,6764
-biopipen/scripts/tcr/Immunarch-kmer.R,sha256=autd1IeFEgWpidg7o2tMVT6T8qDeqgIwLF_KyYmBMvU,6171
-biopipen/scripts/tcr/Immunarch-overlap.R,sha256=zqQEgINJpwPP-WnTRA3GxFfKUOFxwmGCt_qIcT_Qndc,7418
-biopipen/scripts/tcr/Immunarch-spectratyping.R,sha256=QFky_PqKYGAI-4-4UY7MoU7HitBImjHqFnxYaW5wQq0,2850
-biopipen/scripts/tcr/Immunarch-tracking.R,sha256=Itqyq2j14vtdJldaSkbx4H389a_UcHpQjD-icXB-WMU,4336
-biopipen/scripts/tcr/Immunarch-vjjunc.R,sha256=ipOU2ShjUQQSojWgBqRpCvG82Cv09qySAq0DiimHygc,4400
+biopipen/scripts/tcr/Immunarch-basic.R,sha256=err_gEKyx6OcxhbP2GVSaNV-mNlwHlrzxZJbUp2NiNY,3289
+biopipen/scripts/tcr/Immunarch-clonality.R,sha256=d2C1qzxRcnHE4ROF9DvXCnlKH3aK7tYRNDI-31A7A1o,3939
+biopipen/scripts/tcr/Immunarch-diversity.R,sha256=yhYL6G9M7Pxr3U3kx0ZgTn_WCqj5DiFpq2pY4NQlbW4,27804
+biopipen/scripts/tcr/Immunarch-geneusage.R,sha256=MvBmGYRmQD3uKlYe-cheXNm2pK13Ck-bgwe0HG7D0MA,7496
+biopipen/scripts/tcr/Immunarch-kmer.R,sha256=IBb5-R-N6PW9jqTZEFWYmy_lgcJQLZL-osLi1vGBxEo,6802
+biopipen/scripts/tcr/Immunarch-overlap.R,sha256=EzAHPY1GFHEkEg4FJoBABzWg9fARLRtEf3ZuNb37qXg,8126
+biopipen/scripts/tcr/Immunarch-spectratyping.R,sha256=dR4p8NkJbtaF2JNyKbVrBofItj5ewPfvXR6sXPTKoWs,3172
+biopipen/scripts/tcr/Immunarch-tracking.R,sha256=LnqNRn77LDi1IKH_2CT5-w4-d4lhYqLV1SSVP7X-Wk4,4582
+biopipen/scripts/tcr/Immunarch-vjjunc.R,sha256=HzEwAVZ6yc8mIE5Q5G42SAwj-VKxAIrFICUPv3PQ5GA,5772
 biopipen/scripts/tcr/Immunarch.R,sha256=MvkWbSYeevZAtyjrztWm6Kaw58SZqK_HpPyrL9JYq1k,4804
 biopipen/scripts/tcr/Immunarch2VDJtools.R,sha256=QB9ILGbnsfoWaRANK6ceb14wpSWy8F1V1EdEmfIqiks,706
 biopipen/scripts/tcr/ImmunarchFilter.R,sha256=xVuBa38SPQ7qSSynDwvyuYljs1M0yKaIhCQ2eWE3vOc,3995
 biopipen/scripts/tcr/ImmunarchLoading.R,sha256=Vw2oIza3mDJzg9kuo-w5jvwdivk4AtDA6oF1RG1Sva8,5776
 biopipen/scripts/tcr/ImmunarchSplitIdents.R,sha256=FGCeGV0uSmFU91lKkldUAeV4A2m3hHw5X4GNi8ffGzI,1873
 biopipen/scripts/tcr/SampleDiversity.R,sha256=oipN4-2nQZe8bYjI0lZ0SvZ7T8GZ_FWkpkobi1cwmWE,2664
-biopipen/scripts/tcr/TCRClusterStats.R,sha256=QhXgfKSh27VHO901hDizyGYTXMYFJxW22StchQUq3uE,12906
+biopipen/scripts/tcr/ScRepLoading.R,sha256=WvmZuudav0BAAWe8-m7BVb3KsOIS0o2QSfARMobiG6A,4654
+biopipen/scripts/tcr/TCRClusterStats.R,sha256=gW1Xhd_yw5H3QgmO3R-ktKhpJZavyWh2zi-PrGq9nQA,13538
 biopipen/scripts/tcr/TCRClustering.R,sha256=Lt_e32c52gJ9fz1abboGXLIR--Lx2dqW0oFlSOCrCVs,10079
-biopipen/scripts/tcr/TCRDock.py,sha256=jjzxMWp-hs0LDtA1mVbiWDvUieSO7X-F9yeKGy1LSTM,3026
-biopipen/scripts/tcr/TESSA.R,sha256=XFC2P_e_Gm83jG5EjzVIW6KcyG5IieAaK7sXDA3_oZ0,6864
+biopipen/scripts/tcr/TCRDock.py,sha256=Oyw27k6vr0pnJ0w1-lrk5b6sZ_IOf6TmbhSxQae-3Q8,3148
+biopipen/scripts/tcr/TESSA.R,sha256=XiAWCLjvzmrb6t0zGybNsRGK9LC-esgNY30ZlycSwS0,7022
 biopipen/scripts/tcr/TESSA_source/Atchley_factors.csv,sha256=SumqDOqP67P54uM7Cuc5_O_rySTWcGo7eX3psMSPX9s,763
 biopipen/scripts/tcr/TESSA_source/BriseisEncoder.py,sha256=z4_Q_6StymffuUGGjHP1-B3aTsXtamKao5Q1-Kg9has,6831
 biopipen/scripts/tcr/TESSA_source/MCMC_control.R,sha256=93Nnz0IG8KfFnVscZDvmBp1qccZoSoG_jIVpOWBQLHE,2911
@@ -251,46 +258,48 @@ biopipen/scripts/tcr/TESSA_source/update.R,sha256=kVrf6zgIkhhiQ2O55XGmxm_DGBKSpc
 biopipen/scripts/tcr/TESSA_source/utility.R,sha256=6qbkMV7yp4bgQe718QiASQUAgOE2euiLgAXOeSqrvHQ,374
 biopipen/scripts/tcr/VJUsage.R,sha256=LjHEbAHW3WriCYiM9-T6Esd4jc6pnoiSxBKTN_YA490,437
 biopipen/scripts/tcr/immunarch-patched.R,sha256=6OAaV6arDVSI409VHuh1oMCuxlMQp-EaM-kkF-sTlCI,7007
-biopipen/scripts/tcr/vdjtools-patch.sh,sha256=rL5qp2S18CrpqduKkeR1HVmmuWhCVJOMKJXvWiKdYIc,566
-biopipen/scripts/vcf/BcftoolsAnnotate.py,sha256=iS-T6IhumqePW5kdyi_Tb6rubyIiCMjSTIRkGL_ad-U,2582
-biopipen/scripts/vcf/BcftoolsFilter.py,sha256=AdQMXFTNLCS5eqYWMNIMbkK8qXJ5j8GYm7HdPopVk0c,2573
-biopipen/scripts/vcf/BcftoolsSort.py,sha256=tU0pTrEIB-7x6iOSfU-KpYY1rEidi6Q4179NntY3cGc,3778
-biopipen/scripts/vcf/BcftoolsView.py,sha256=Sj3KkYPpwQFo5kmZC5MRxItrSE5KVZi0jNYrRFck3Ow,2465
+biopipen/scripts/tcr/vdjtools-patch.sh,sha256=-gJFPVqzzFLdet3q2hccB8gSztRawLV1AnqNp1ZzHOg,568
+biopipen/scripts/vcf/BcftoolsAnnotate.py,sha256=12-VUSP0kl0iyxvahhiu1CDyYJ9nTgGo5RWWVKhkBN8,2615
+biopipen/scripts/vcf/BcftoolsFilter.py,sha256=vh6KjxHdt1JJB7vU39ZH0PqGcdt76VK2EglhoA0WQNM,2598
+biopipen/scripts/vcf/BcftoolsMerge.py,sha256=KpCcEKNtDOEn8n0qSyWpi-lFv1qjnwqJRUlWNrXaqaU,989
+biopipen/scripts/vcf/BcftoolsSort.py,sha256=Gq7d3q7B-YFWw9wE9AO-nL_T5RDckSj-8oCcbsv3yq8,3799
+biopipen/scripts/vcf/BcftoolsView.py,sha256=tFOXskcR3gH576WZNvDcfjBLuzdAztdD1AnxmRTFUA4,2490
 biopipen/scripts/vcf/TruvariBench.sh,sha256=5M7lZhO4laNJvCVCHudf8DYArKNXoiPWuSkXgRi2t_A,908
 biopipen/scripts/vcf/TruvariBenchSummary.R,sha256=rdNNIPoiwqnK6oEOlQUUhnL1MF958W_nDjRCkA5ubz4,1516
 biopipen/scripts/vcf/TruvariConsistency.R,sha256=6h20v8qztbl1KZInJwoSK_t5XwqhKMTMzPWNPhoAjlM,2314
-biopipen/scripts/vcf/Vcf2Bed.py,sha256=LzyJ9qW1s5mbfF8maLc77_0rE98KMc2lq1R94_NFbSU,855
-biopipen/scripts/vcf/VcfAnno.py,sha256=FW626rAs_WSU7AHQMKjfkYoByUGh_gVyJM97neGfOMo,802
-biopipen/scripts/vcf/VcfDownSample.sh,sha256=yBlyoA8xyHPkVc1XAs1biNZmN7rDR-CMz8qVh2GGvuk,939
-biopipen/scripts/vcf/VcfFilter.py,sha256=0clQi9XuN0B33xAquQ3e7ce1PZlzIOmOFctNA-dpdEw,1881
-biopipen/scripts/vcf/VcfFix.py,sha256=r2bgwwb2hAMr42wjpFZSFcUDxGllvhkOaRY_r9sKLNE,1304
-biopipen/scripts/vcf/VcfFix_utils.py,sha256=Ur1-nFFYYjg7HYiK_C6Is_MTZXFULKRTwTGqBD8jzyU,2299
-biopipen/scripts/vcf/VcfIndex.py,sha256=kMOdB8O4UWvvxeEnAa3iZoH7_ySKHCJ0LOpEds0GXf4,635
-biopipen/scripts/vcf/VcfIntersect.py,sha256=6u9tLlfmEhlSMkYLXurVOO2uU94JwKRegSHhCzliHX0,735
-biopipen/scripts/vcf/VcfLiftOver.sh,sha256=-mb-aY0kbr62Audm8urEh3iLef_FREVWgt8hs3ELNK8,565
-biopipen/scripts/vcf/VcfSplitSamples.py,sha256=GraKi7WluzDAvVVGljwd3Yif6MriniF8stZOmllZtgk,1528
-biopipen/scripts/vcf/bcftools_utils.py,sha256=p91rZp0RG6AtbpYA_KuKCfa6T5aNKMq_rK95QPL7mMI,1514
-biopipen/scripts/web/Download.py,sha256=WKC_t5ZEeJoKFyY9XwksHARcMbKmHMcxNEUDLMGJ0Cc,924
-biopipen/scripts/web/DownloadList.py,sha256=cZvdi3LVzlATiTvAXe0uuDDXGqB5jcR2zHrMLCEb2U8,1130
-biopipen/scripts/web/GCloudStorageDownloadBucket.py,sha256=DBPfQaIpm-W7-uBHZjwOqP_FaWLW9aIFooVnmfvTAa4,2657
-biopipen/scripts/web/GCloudStorageDownloadFile.py,sha256=tZIZpDvWQyEhY4qIlRDF1NYRT-Ums8cIgElp00F0uz4,823
-biopipen/scripts/web/gcloud_common.py,sha256=fLhW8eiBUSjn9scQzu3IQC_IFvFO3r_K3f8fTqxWEBw,1238
+biopipen/scripts/vcf/Vcf2Bed.py,sha256=E0Bu7uqKhCPoikD_hM9dgNtzrjgZPQiPPSruULAlz4E,879
+biopipen/scripts/vcf/VcfAnno.py,sha256=cxLVTmJ-U2zlz3dUys2xzdQ6oXaHNOZY6AlHGynyZv4,1003
+biopipen/scripts/vcf/VcfDownSample.sh,sha256=_lI8or4uXqTHbawM2eQ4fxH3EuffaNtU9c3i68_aKAA,1343
+biopipen/scripts/vcf/VcfFilter.py,sha256=KRMfuARccXr2uAXkEB4KKUwhC7AEVOVM-1_THcDugqQ,1952
+biopipen/scripts/vcf/VcfFix.py,sha256=UohgLNRK8PFL5cHP8LqLWl2LjUAo1v5Bvsbr2nzj2L8,1330
+biopipen/scripts/vcf/VcfFix_utils.py,sha256=pQbeTBUWddnegRizdljMaeKJWr-ew0IWE3Oa9lsJKWo,2443
+biopipen/scripts/vcf/VcfIndex.py,sha256=LRjNBiQOoiuQYJvwVIvOSi66urfG0EQl9-nrWMlx2dQ,655
+biopipen/scripts/vcf/VcfIntersect.py,sha256=XmQoehPX6fsfYl7rJu-BGzG6InM11z-RXBUMw32qnPU,751
+biopipen/scripts/vcf/VcfLiftOver.sh,sha256=mZYTcimXKNw1QfekPuHLu15_cQXdHXK4rQmyMas3Usk,705
+biopipen/scripts/vcf/VcfSplitSamples.py,sha256=56VwFdzK2wpQoNRS66siUlJD39QAzg8emdw5AR5hRo8,1558
+biopipen/scripts/vcf/bcftools_utils.py,sha256=LtqchPmnZG4uY9k0llT5NemhK6QPwduGGYc17UJj6uo,1562
+biopipen/scripts/web/Download.py,sha256=sAXBAFWKostwrD5yb2b2QcrsWCIO-D_s8KFwlBdCISg,1061
+biopipen/scripts/web/DownloadList.py,sha256=_LqebncRvk29czkYMyKnJG9oRqRM-GIoRqgiRhkbvfI,1169
+biopipen/scripts/web/GCloudStorageDownloadBucket.py,sha256=EnjEnCL52-X8v8d5tMvhJtJ777bQWKYUk19ISpXVVV0,2696
+biopipen/scripts/web/GCloudStorageDownloadFile.py,sha256=2txA7W0AfnnuyocZtLp20I-RFAF2dCbL8sL7NzKkiyI,839
+biopipen/scripts/web/gcloud_common.py,sha256=rMa42CRw3iJGV1OnG8A2KqLWFp8BocCH2nXRgkNSh1A,1254
 biopipen/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/utils/caching.R,sha256=qANQqH8p-VpvD8V4VSoqSfp0TFr4esujC7x3OFZsJMw,1687
 biopipen/utils/common_docstrs.py,sha256=Ow-g-yS5P7DEO37cP1X-xioRbYWygfQHxIuLIaDdrjs,6288
 biopipen/utils/gene.R,sha256=EITppeN7dwXy7LnFELYHeRCSHImYno0JncLyVWEAXOM,3757
 biopipen/utils/gene.py,sha256=ToRgAPYc8E72Hm6uYi84ImQaRMPZp5rN7O4CxK7vCag,4477
-biopipen/utils/gsea.R,sha256=BUr4pwfo7ZyinOyNa4O4dDxA1c50qWb3lpph374Yw_A,9239
+biopipen/utils/gsea.R,sha256=GaaUTW0t0S6Y_Pk9I17MKRq01ccIPI4J03y0l0TM32Q,11000
 biopipen/utils/io.R,sha256=jIYdqdn0iRWfQYAZa5CjXi3fikqmYvPPLIXhobRe8sw,537
-biopipen/utils/misc.R,sha256=qTninxi9XAM_3QJqwThflGA-j7p1aKpQ9Pjmix6Iy3U,12059
-biopipen/utils/misc.py,sha256=nkQHa3GMc7Ce0N2GKmucbRc8BMXgZ2yr_SPbq9RYA4s,3740
+biopipen/utils/misc.R,sha256=QkJPlM2Ae0wJHVR0hQglfTBzOCyXElR104zuCZZXHjI,18356
+biopipen/utils/misc.py,sha256=pDZ-INWVNqHuXYvcjmu8KqNAigkh2lsHy0BxX44CPvc,4048
 biopipen/utils/mutate_helpers.R,sha256=Bqy6Oi4rrPEPJw0Jq32bVAwwBfZv7JJL9jFcK5x-cek,17649
-biopipen/utils/plot.R,sha256=fmWnCv6EpOU8NvHFvShbdPRqB659vHcDlJAqWIXM8XQ,4415
-biopipen/utils/reference.py,sha256=oi5evicLwHxF0KAIPNZohBeHJLJQNWFJH0cr2y5pgcg,5873
+biopipen/utils/plot.R,sha256=ijqVU68W_jl27YHSuHSFekOSvTus97mRCqpbri_2an4,5880
+biopipen/utils/reference.py,sha256=Oc6IlA1giLxymAuI7DO-IQLHQ7-DbsWzOQE86oTDfMU,5955
+biopipen/utils/repr.R,sha256=GO5F5FFE4XjFXO5JODAJ7Nwvr00yiPMG34vIPMkKkrU,4016
 biopipen/utils/rnaseq.R,sha256=Ro2B2dG-Z2oVaT5tkwp9RHBz4dp_RF-JcizlM5GYXFs,1298
 biopipen/utils/single_cell.R,sha256=3jmTV9-kHTXyBA6GRlRf_Ig0jx_5jRr6E1THoa1869k,7564
-biopipen/utils/vcf.py,sha256=ajXs0M_QghEctlvUlSRjWQIABVF02wPdYd-0LP4mIsU,9377
-biopipen-0.32.1.dist-info/METADATA,sha256=vaxY3m7PF1adjEsggWE8SmU2rPHtRS0-t-23r7xkgUo,933
-biopipen-0.32.1.dist-info/WHEEL,sha256=Nq82e9rUAnEjt98J6MlVmMCZb-t9cYE2Ir1kpBmnWfs,88
-biopipen-0.32.1.dist-info/entry_points.txt,sha256=BYqHGBQJxyFDNLYqgH64ycI5PYwnlqwYcCFsMvJgzAU,653
-biopipen-0.32.1.dist-info/RECORD,,
+biopipen/utils/vcf.py,sha256=MmMbAtLUcKPp02jUdk9TzuET2gWSeoWn7xgoOXFysK0,9393
+biopipen-0.33.0.dist-info/METADATA,sha256=J_5O1LtSrQUaYsnmwkw8Hh9IjwULZZGlsmGfbWJU6lc,930
+biopipen-0.33.0.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
+biopipen-0.33.0.dist-info/entry_points.txt,sha256=BYqHGBQJxyFDNLYqgH64ycI5PYwnlqwYcCFsMvJgzAU,653
+biopipen-0.33.0.dist-info/RECORD,,

{biopipen-0.32.1.dist-info → biopipen-0.33.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.9.1
+Generator: poetry-core 2.1.1
 Root-Is-Purelib: true
 Tag: py3-none-any

biopipen/scripts/scrna/SeuratClusterStats-hists.R

@@ -1,139 +0,0 @@
-# Loaded variables: srtfile, outdir, srtobj
-
-# hists_defaults <- {{envs.hists_defaults | r: todot="-"}}
-# hists <- {{envs.hists | r: todot="-", skip=1}}
-log_info("hists:")
-
-do_one_hists <- function(m, case, odir, h1, each = NULL) {
-    ofile <- file.path(odir, paste0(slugify(h1), ifelse(is.null(each), "", paste0("-", slugify(each))), ".png"))
-
-    p <- ggplot(m, aes(x=!!sym(case$x))) +
-        geom_histogram(
-            bins = case$bins,
-            fill = "white",
-            color = "#3a9ddc",
-            stat = ifelse(is.numeric(m[[case$x]]), "bin", "count")
-        ) +
-        theme_prism() +
-        xlab(case$x) +
-        ylab("Number of cells")
-
-    if (!is.null(case$cells_by)) {
-        p <- p + facet_wrap(vars(!!sym(case$cells_by)), ncol = case$ncol, drop = FALSE)
-        ngroups <- length(unique(m[[case$cells_by]]))
-    } else {
-        ngroups <- 1
-    }
-
-    if (!is.null(case$plus) && length(case$plus) > 0) {
-        for (pl in case$plus) {
-            p <- p + eval(parse(text=pl))
-        }
-    }
-
-    devpars <- case$devpars
-    if (is.null(devpars$res)) { devpars$res <- 100 }
-    if (is.null(devpars$width)) {
-        devpars$width <- ifelse(ngroups == 1, 600, 300 * min(ngroups, case$ncol)) }
-    if (is.null(devpars$height)) {
-        devpars$height <- ifelse(ngroups == 1, 300, 150 * ceiling(ngroups / case$ncol))
-    }
-    png(ofile, width=devpars$width, height=devpars$height, res=devpars$res)
-    print(p)
-    dev.off()
-
-    # Add report
-    if (!is.null(each)) {
-        add_report(
-            list(src = ofile, descr = first(m[[case$each]])),
-            h1 = h1,
-            ui = "table_of_images"
-        )
-    } else {
-        add_report(
-            list(kind = "image", src = ofile),
-            h1 = h1
-        )
-    }
-}
-
-if (is.null(hists) || length(hists) == 0) {
-    log_warn("- no cases specified, skipping ...")
-} else {
-
-    for (name in names(hists)) {
-        hists[[name]] <- list_update(hists_defaults, hists[[name]])
-        case <- hists[[name]]
-
-        odir <- file.path(outdir, "hists", slugify(name))
-        dir.create(odir, recursive=TRUE, showWarnings=FALSE)
-
-        h1 <- name
-        if (!is.null(case$subset)) {
-            meta <- srtobj@meta.data %>% filter(!!rlang::parse_expr(case$subset))
-        } else {
-            meta <- srtobj@meta.data
-        }
-
-        if (is.null(case$x)) { stop("`x` must be specified for hists.") }
-
-        meta <- meta %>% drop_na(!!sym(case$x))
-        if (!is.null(case$cells_by)) { meta <- meta %>% drop_na(!!sym(case$cells_by)) }
-        if (!is.null(case$each)) { meta <- meta %>% drop_na(!!sym(case$each)) }
-        if (!is.null(case$x_order) && length(case$x_order) > 0) {
-            meta <- meta %>% filter(!!sym(case$x) %in% case$x_order) %>%
-                arrange(match(!!sym(case$x), case$x_order))
-        }
-        if (!is.null(case$cells_order) && length(case$cells_order) > 0) {
-            if (is.null(case$cells_by)) { stop("`cells_by` must be specified for `cells_order`.") }
-            meta <- meta %>% filter(!!sym(case$cells_by) %in% case$cells_order) %>%
-                arrange(match(!!sym(case$cells_by), case$cells_order))
-        } else if (!is.null(case$cells_orderby)) {
-            meta <- meta %>% arrange(!!parse_expr(case$cells_orderby))
-            cell_groups <- meta %>% pull(!!sym(case$cells_by)) %>% unique()
-            meta <- meta %>% filter(!!sym(case$cells_by) %in% cell_groups[1:case$cells_n])
-            meta[[case$cells_by]] <- factor(meta[[case$cells_by]], levels=cell_groups[1:case$cells_n])
-        }
-
-        if (!is.null(case$each)) {
-            eachs <- meta %>% pull(!!sym(case$each)) %>% unique()
-            add_report(
-                list(
-                    kind = "descr",
-                    content = paste0(
-                        "Histogram showing number of cells ",
-                        ifelse(is.null(case$cells_by), "", paste0("by <code>", case$cells_by, "</code> ")),
-                        "in each <code>",
-                        case$each,
-                        "</code> along <code>",
-                        case$x,
-                        "</code>"
-                    )
-                ),
-                h1 = h1
-            )
-            for (each in eachs) {
-                log_info("- Case: {h1} - {each} ...")
-                m <- meta %>% filter(!!sym(case$each) == each)
-                do_one_hists(m, case, odir, h1, each)
-            }
-        } else {
-            log_info("- Case: {h1} ...")
-            add_report(
-                list(
-                    kind = "descr",
-                    content = paste0(
-                        "Histogram showing number of cells ",
-                        ifelse(is.null(case$cells_by), "", paste0("by <code>", case$cells_by, "</code> ")),
-                        "along <code>",
-                        case$x,
-                        "</code>"
-                    )
-                ),
-                h1 = h1
-            )
-            do_one_hists(meta, case, odir, h1)
-        }
-    }
-
-}