biopipen 0.7.0__py3-none-any.whl → 0.8.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Potentially problematic release.
This version of biopipen might be problematic. Click here for more details.
- biopipen/__init__.py +1 -1
- biopipen/core/config.py +0 -5
- biopipen/core/config.toml +4 -4
- biopipen/core/defaults.py +3 -3
- biopipen/core/filters.py +1 -0
- biopipen/core/proc.py +1 -3
- biopipen/core/testing.py +1 -2
- biopipen/ns/bam.py +10 -14
- biopipen/ns/bcftools.py +37 -7
- biopipen/ns/bed.py +9 -16
- biopipen/ns/cnv.py +8 -11
- biopipen/ns/cnvkit.py +32 -59
- biopipen/ns/cnvkit_pipeline.py +266 -310
- biopipen/ns/csv.py +0 -2
- biopipen/ns/gene.py +0 -1
- biopipen/ns/gsea.py +4 -10
- biopipen/ns/misc.py +0 -5
- biopipen/ns/plot.py +2 -4
- biopipen/ns/rnaseq.py +0 -1
- biopipen/ns/scrna.py +78 -120
- biopipen/ns/scrna_metabolic_landscape.py +306 -348
- biopipen/ns/tcgamaf.py +52 -0
- biopipen/ns/tcr.py +5 -15
- biopipen/ns/vcf.py +52 -34
- biopipen/ns/web.py +8 -19
- biopipen/reports/bam/CNAClinic.svelte +1 -1
- biopipen/reports/bam/CNVpytor.svelte +2 -2
- biopipen/reports/bam/ControlFREEC.svelte +1 -1
- biopipen/reports/cnv/AneuploidyScore.svelte +2 -2
- biopipen/reports/cnv/AneuploidyScoreSummary.svelte +1 -1
- biopipen/reports/cnvkit/CNVkitDiagram.svelte +1 -1
- biopipen/reports/cnvkit/CNVkitHeatmap.svelte +1 -1
- biopipen/reports/cnvkit/CNVkitScatter.svelte +1 -1
- biopipen/reports/gsea/FGSEA.svelte +1 -1
- biopipen/reports/gsea/GSEA.svelte +2 -2
- biopipen/reports/scrna/CellsDistribution.svelte +1 -1
- biopipen/reports/scrna/DimPlots.svelte +1 -1
- biopipen/reports/scrna/GeneExpressionInvistigation.svelte +1 -1
- biopipen/reports/scrna/MarkersFinder.svelte +42 -39
- biopipen/reports/scrna/ScFGSEA.svelte +3 -3
- biopipen/reports/scrna/SeuratClusterStats.svelte +3 -3
- biopipen/reports/scrna/SeuratPreparing.svelte +2 -2
- biopipen/reports/scrna_metabolic_landscape/MetabolicFeaturesIntraSubsets.svelte +2 -2
- biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte +1 -1
- biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.svelte +1 -1
- biopipen/reports/tcr/CloneResidency.svelte +4 -4
- biopipen/reports/tcr/Immunarch.svelte +2 -2
- biopipen/reports/tcr/SampleDiversity.svelte +2 -2
- biopipen/reports/tcr/TCRClusteringStats.svelte +3 -3
- biopipen/reports/tcr/VJUsage.svelte +1 -1
- biopipen/reports/utils/gsea.liq +1 -1
- biopipen/reports/utils/misc.liq +1 -1
- biopipen/reports/vcf/TruvariBenchSummary.svelte +1 -1
- biopipen/reports/vcf/TruvariConsistency.svelte +3 -3
- biopipen/scripts/bcftools/BcftoolsSort.py +19 -0
- biopipen/scripts/scrna/MarkersFinder.R +73 -35
- biopipen/scripts/tcgamaf/Maf2Vcf.py +22 -0
- biopipen/scripts/tcgamaf/MafAddChr.py +14 -0
- biopipen/scripts/tcgamaf/maf2vcf.pl +427 -0
- biopipen/scripts/vcf/VcfAnno.py +26 -0
- biopipen/scripts/vcf/VcfFix_utils.py +3 -2
- {biopipen-0.7.0.dist-info → biopipen-0.8.0.dist-info}/METADATA +7 -8
- {biopipen-0.7.0.dist-info → biopipen-0.8.0.dist-info}/RECORD +65 -59
- {biopipen-0.7.0.dist-info → biopipen-0.8.0.dist-info}/WHEEL +1 -1
- {biopipen-0.7.0.dist-info → biopipen-0.8.0.dist-info}/entry_points.txt +2 -1
|
@@ -1,64 +1,66 @@
|
|
|
1
|
-
biopipen/__init__.py,sha256=
|
|
1
|
+
biopipen/__init__.py,sha256=kTBVFU2JV0uZaCX5p4I2Yj-xBdwAAjn3KIWXhA0k2Fw,23
|
|
2
2
|
biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
|
|
3
|
-
biopipen/core/config.py,sha256=
|
|
4
|
-
biopipen/core/config.toml,sha256=
|
|
5
|
-
biopipen/core/defaults.py,sha256=
|
|
6
|
-
biopipen/core/filters.py,sha256=
|
|
7
|
-
biopipen/core/proc.py,sha256=
|
|
8
|
-
biopipen/core/testing.py,sha256=
|
|
3
|
+
biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
|
|
4
|
+
biopipen/core/config.toml,sha256=sEpvNX31ZL0XF2OpJ5tk_YJzLTwjkTf0I8-TvUfXQ3o,1598
|
|
5
|
+
biopipen/core/defaults.py,sha256=yPeehPLk_OYCf71IgRVCWuQRxLAMixDF81Ium0HtPKI,344
|
|
6
|
+
biopipen/core/filters.py,sha256=dJuCIrWKt7ZaHD9FPyZr65f2y9kfS2k341ayOdRefy0,2360
|
|
7
|
+
biopipen/core/proc.py,sha256=enxk0Zq_UX-C62LjRk0AhS2e8B-NjvKt2rrqdTGHbe8,498
|
|
8
|
+
biopipen/core/testing.py,sha256=7dC_knI-DzRtHoyEisQ73cGTNQb_kvVdMb3rDgQ4Qng,1586
|
|
9
9
|
biopipen/ns/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
|
|
10
|
-
biopipen/ns/bam.py,sha256=
|
|
11
|
-
biopipen/ns/bcftools.py,sha256=
|
|
12
|
-
biopipen/ns/bed.py,sha256=
|
|
13
|
-
biopipen/ns/cnv.py,sha256=
|
|
14
|
-
biopipen/ns/cnvkit.py,sha256=
|
|
15
|
-
biopipen/ns/cnvkit_pipeline.py,sha256=
|
|
16
|
-
biopipen/ns/csv.py,sha256=
|
|
17
|
-
biopipen/ns/gene.py,sha256=
|
|
18
|
-
biopipen/ns/gsea.py,sha256=
|
|
19
|
-
biopipen/ns/misc.py,sha256=
|
|
20
|
-
biopipen/ns/plot.py,sha256=
|
|
21
|
-
biopipen/ns/rnaseq.py,sha256=
|
|
22
|
-
biopipen/ns/scrna.py,sha256=
|
|
23
|
-
biopipen/ns/scrna_metabolic_landscape.py,sha256=
|
|
24
|
-
biopipen/ns/
|
|
25
|
-
biopipen/ns/
|
|
26
|
-
biopipen/ns/
|
|
27
|
-
biopipen/
|
|
28
|
-
biopipen/reports/bam/
|
|
29
|
-
biopipen/reports/bam/
|
|
30
|
-
biopipen/reports/
|
|
31
|
-
biopipen/reports/cnv/
|
|
32
|
-
biopipen/reports/
|
|
33
|
-
biopipen/reports/cnvkit/
|
|
34
|
-
biopipen/reports/cnvkit/
|
|
35
|
-
biopipen/reports/
|
|
36
|
-
biopipen/reports/gsea/
|
|
37
|
-
biopipen/reports/
|
|
38
|
-
biopipen/reports/scrna/
|
|
39
|
-
biopipen/reports/scrna/
|
|
40
|
-
biopipen/reports/scrna/
|
|
41
|
-
biopipen/reports/scrna/
|
|
42
|
-
biopipen/reports/scrna/
|
|
43
|
-
biopipen/reports/scrna/
|
|
10
|
+
biopipen/ns/bam.py,sha256=fqxcxeyuwMMc2yOII7ql6YrlD0gIAtxFwbn1fjuWi_o,6484
|
|
11
|
+
biopipen/ns/bcftools.py,sha256=puCDfIL-1z6cz2y1Rlz-ESNIr8xJgeIjEQ440qicCvM,3467
|
|
12
|
+
biopipen/ns/bed.py,sha256=h3lG28f_1MgbvPRBTtzKeG0iNhFkhSj4sre_NtgTwpg,5231
|
|
13
|
+
biopipen/ns/cnv.py,sha256=j-QB3zCcCQkadKzBA-wP2oPOndM-Yigiq85U7-PXGAg,2901
|
|
14
|
+
biopipen/ns/cnvkit.py,sha256=gLY9kFjmFNI4nTk4SLzkvRAL27msg7nANvZIMeVL9wM,28348
|
|
15
|
+
biopipen/ns/cnvkit_pipeline.py,sha256=TeU1KjnSd7bswtPHFzT2_4VmjEZOmrqLuZMpnfgCv10,26835
|
|
16
|
+
biopipen/ns/csv.py,sha256=x6J7WePX_hKSTxS1Ou4_o_oJJZaGN5a2E0Qve8R1QJc,484
|
|
17
|
+
biopipen/ns/gene.py,sha256=Q5FzRByfnRITXRNRZR65ApG09FRyiihRC3TcIXxufzE,2228
|
|
18
|
+
biopipen/ns/gsea.py,sha256=rM_Klmta2C4IxIzJi4T_SjQSBHzRNaoQELWRWH-m-QM,7423
|
|
19
|
+
biopipen/ns/misc.py,sha256=GPrqizuVFttLGDsSGYSkd-F03ZZ4amu3qHVe94sQLmM,3015
|
|
20
|
+
biopipen/ns/plot.py,sha256=AoInrMSe7b1Pjorgy4f1LMkaTwDmumkTzJDI4YyRbgs,4026
|
|
21
|
+
biopipen/ns/rnaseq.py,sha256=l4vFeRasGhkexopGTM_VfSyIFewOxg-9L5niFzhWUNA,565
|
|
22
|
+
biopipen/ns/scrna.py,sha256=jW4ZQm7jiA4zNVXS2JPsOBBwQkhGLnT2JpxA3Py_vyg,28935
|
|
23
|
+
biopipen/ns/scrna_metabolic_landscape.py,sha256=A-YSrlezuoA6FUPOqMaA4VrGOLDa_FOUyh1hjEmvgQY,15622
|
|
24
|
+
biopipen/ns/tcgamaf.py,sha256=AFbUJIxiMSvsVY3RcHgjRFuMnNh2DG3Mr5slLNEyz6o,1455
|
|
25
|
+
biopipen/ns/tcr.py,sha256=GHwQDydqIMg8hGynmd8QzzCLLfQg-VMRfR-0QctoSUg,23074
|
|
26
|
+
biopipen/ns/vcf.py,sha256=cdkKroii0_nl_bSP2cnO09qESUAhHqu6btOiTSKS79Y,15314
|
|
27
|
+
biopipen/ns/web.py,sha256=3zucrDo-IVsSnIvlw-deoScuxqWa6OMTm8Vo-R4E44Q,2224
|
|
28
|
+
biopipen/reports/bam/CNAClinic.svelte,sha256=UYrh5vok4BgQbv5b1iohpoJKbBXQCAWx4RyOI-2m7og,212
|
|
29
|
+
biopipen/reports/bam/CNVpytor.svelte,sha256=afJSkCHGYDKsxj_mv2BqIOadmgEeONVkR9uGmRR15dM,1363
|
|
30
|
+
biopipen/reports/bam/ControlFREEC.svelte,sha256=3XKUKEaKWmOsYrHU90w4so5Fypr8YYC1MlMyJ2gMtFM,836
|
|
31
|
+
biopipen/reports/cnv/AneuploidyScore.svelte,sha256=iaLBRO-VjPmYEOhLqA7lcTlGw15-LCJbsqsZWrmqziE,1019
|
|
32
|
+
biopipen/reports/cnv/AneuploidyScoreSummary.svelte,sha256=sBYqRLLg4UpLuTFmv8nWn9BbnJL4muNjW0mi574Ym5M,1129
|
|
33
|
+
biopipen/reports/cnvkit/CNVkitDiagram.svelte,sha256=SQU0ldaUtKXFYyPykxqaUofHfbuE1rNEzAUfJxZ7yz4,466
|
|
34
|
+
biopipen/reports/cnvkit/CNVkitHeatmap.svelte,sha256=tXPejQCdTnCH9DS1TQmTEcnUJ54dAQKo_I8CJvDrUkI,518
|
|
35
|
+
biopipen/reports/cnvkit/CNVkitScatter.svelte,sha256=SQU0ldaUtKXFYyPykxqaUofHfbuE1rNEzAUfJxZ7yz4,466
|
|
36
|
+
biopipen/reports/gsea/FGSEA.svelte,sha256=u5dPpS1oKAbF74lGVLDCoe_V8UY2ADMy5AlN03RtS1k,404
|
|
37
|
+
biopipen/reports/gsea/GSEA.svelte,sha256=bSwWKENA9AyGurfVMAHLEXFNLs7axv1WHRrvy9LuEfQ,416
|
|
38
|
+
biopipen/reports/scrna/CellsDistribution.svelte,sha256=Q5v1V50EIAO7HMTm_uKQM367TU7d871UMxRHNUNQSys,581
|
|
39
|
+
biopipen/reports/scrna/DimPlots.svelte,sha256=sDSv4bLaEaTbgDJFuiogkVplU9PbZD3BcQKKykukgR8,478
|
|
40
|
+
biopipen/reports/scrna/GeneExpressionInvistigation.svelte,sha256=GavmYimO4EDdAaR8TZBWmQlRXLi4EC8LZpFIvJkockE,792
|
|
41
|
+
biopipen/reports/scrna/MarkersFinder.svelte,sha256=6-RX-qIDng0k-Dcl1X2dLUunyQjbRAQePYCE7IYajRE,1801
|
|
42
|
+
biopipen/reports/scrna/ScFGSEA.svelte,sha256=UXhUSGXHrzkUzFkvc9-SR5R1SlHxutgA3r7gFtvj2Xg,1040
|
|
43
|
+
biopipen/reports/scrna/SeuratClusterStats.svelte,sha256=aztYcWy4BWAXg00aQ0-J29ybM1A8yW96bpXAr9OclSI,4970
|
|
44
|
+
biopipen/reports/scrna/SeuratPreparing.svelte,sha256=BlxtoUfFgzG-p_E4DJR_8u5f7oFdL3cIQrck2rjqT5c,1180
|
|
44
45
|
biopipen/reports/scrna_metabolic_landscape/MetabolicFeatures.svelte,sha256=1AHjiInGLev1_gfis5oVegYXgKLzDXA9qMwEgPqRDfI,880
|
|
45
|
-
biopipen/reports/scrna_metabolic_landscape/MetabolicFeaturesIntraSubsets.svelte,sha256=
|
|
46
|
-
biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte,sha256=
|
|
47
|
-
biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.svelte,sha256=
|
|
48
|
-
biopipen/reports/tcr/CloneResidency.svelte,sha256=
|
|
49
|
-
biopipen/reports/tcr/Immunarch.svelte,sha256=
|
|
50
|
-
biopipen/reports/tcr/SampleDiversity.svelte,sha256=
|
|
51
|
-
biopipen/reports/tcr/TCRClusteringStats.svelte,sha256=
|
|
52
|
-
biopipen/reports/tcr/VJUsage.svelte,sha256=
|
|
53
|
-
biopipen/reports/utils/gsea.liq,sha256=
|
|
54
|
-
biopipen/reports/utils/misc.liq,sha256=
|
|
55
|
-
biopipen/reports/vcf/TruvariBenchSummary.svelte,sha256=
|
|
56
|
-
biopipen/reports/vcf/TruvariConsistency.svelte,sha256=
|
|
46
|
+
biopipen/reports/scrna_metabolic_landscape/MetabolicFeaturesIntraSubsets.svelte,sha256=RqlrWU_e7O98e23HfUh5-HPElniuOXQ1N_SorHgFPV8,992
|
|
47
|
+
biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayActivity.svelte,sha256=LKDdNf0A5kLK2VJ7o1iMFNS5U1Zd1h1AodwyKwyTvlg,2542
|
|
48
|
+
biopipen/reports/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.svelte,sha256=Kl7FeGG-vfgs8CcLnazuCb692-NP5rHmFekBvRRtyLo,636
|
|
49
|
+
biopipen/reports/tcr/CloneResidency.svelte,sha256=ap6BCAUAm33bV6VieTh59sZwNYdE8BsTx25vU1sRAgw,2928
|
|
50
|
+
biopipen/reports/tcr/Immunarch.svelte,sha256=GjuT6genEO9f6L8tbXQKP3sKa_O90PASfMX1Ig7o74U,7853
|
|
51
|
+
biopipen/reports/tcr/SampleDiversity.svelte,sha256=6qnzpQbLvUtN1wV77nmS6PpzBuIe49sS-qRMkae0IZM,5523
|
|
52
|
+
biopipen/reports/tcr/TCRClusteringStats.svelte,sha256=nbE9i1EUjgQbYF2dxgeZ7x8PJOwTiHBRfJHGBWSJXFM,3756
|
|
53
|
+
biopipen/reports/tcr/VJUsage.svelte,sha256=gTOfOFQ5cH9nbfABauyGfOg7B9KiHHgTYZiLtaM1EGM,425
|
|
54
|
+
biopipen/reports/utils/gsea.liq,sha256=XAaNbX04aEg6ylgAU60PyJM2lHxJ-cisVkYYfT__cqc,2626
|
|
55
|
+
biopipen/reports/utils/misc.liq,sha256=tce8pgg5eeFy51_iX0mT34M5Ykr5bi9kQs6q1oQBJQo,1652
|
|
56
|
+
biopipen/reports/vcf/TruvariBenchSummary.svelte,sha256=l7RXKWzMRjkAwWhdCNpx0hz2sO1nYFJI4xHZdt2haSw,576
|
|
57
|
+
biopipen/reports/vcf/TruvariConsistency.svelte,sha256=VQwNRHMxxXYlYxQpZ0-KrShkElthBP__yWNc1YFOU54,646
|
|
57
58
|
biopipen/scripts/bam/CNAClinic.R,sha256=XH-J_RHMb5zh0jkaIa2UMivi13ckKZTyGWO2NxZRvQc,5000
|
|
58
59
|
biopipen/scripts/bam/CNVpytor.py,sha256=5eeYgdaxOmEXRJtH1ws_CE42QmLYosXlGZln4o_aey0,12296
|
|
59
60
|
biopipen/scripts/bam/ControlFREEC.py,sha256=xePG3UlIdr1hxITcF4nY_LtrBb5B9no_LUCtD6WQZWg,3142
|
|
60
61
|
biopipen/scripts/bcftools/BcftoolsAnnotate.py,sha256=5mdyp7UF11ok37QqnvPVs16_7v2EKmaT8hDpj4EvQhM,1343
|
|
61
62
|
biopipen/scripts/bcftools/BcftoolsFilter.py,sha256=3i8hWAaxAnhIGXbr_uK2Xa9xI_n97eT0gBPXzrkOL2Q,2284
|
|
63
|
+
biopipen/scripts/bcftools/BcftoolsSort.py,sha256=5YYTCsNkE7vqnK9dH9HeBKZUhpc5uxUlyyfGJJmtXoc,549
|
|
62
64
|
biopipen/scripts/bed/Bed2Vcf.py,sha256=6ZXX3TsDNuYHIObFEjEpkr9Uz9TJfXrB5QLVpnpVg2Q,4981
|
|
63
65
|
biopipen/scripts/bed/BedConsensus.py,sha256=PB2lTDFvD7pd3ilXxyd9_-EtxDQODl3RqJsGr6P3ZUQ,6380
|
|
64
66
|
biopipen/scripts/bed/BedLiftOver.sh,sha256=Y4gBsz9w4zhE29UmWojO6F4PXMMMWC1uCzjrxa19eOs,256
|
|
@@ -97,7 +99,7 @@ biopipen/scripts/scrna/ExprImpute-rmagic.R,sha256=CfiCL-agHg2p-rmW7IcySlqblT7Ik2
|
|
|
97
99
|
biopipen/scripts/scrna/ExprImpute-scimpute.R,sha256=mg40qCUW7-nP5oHPvARq7dmtoahM0GRFWXQpum0BXVk,1082
|
|
98
100
|
biopipen/scripts/scrna/ExprImpute.R,sha256=TuyBmK_hH9g4Jb36RHR0y2RQ8TxS9c6htrFaH6Vog3M,307
|
|
99
101
|
biopipen/scripts/scrna/GeneExpressionInvistigation.R,sha256=Qa_Gc_jhvsNCsEmI6bD_cZx8xaHznltTJd8wXt45quY,3760
|
|
100
|
-
biopipen/scripts/scrna/MarkersFinder.R,sha256=
|
|
102
|
+
biopipen/scripts/scrna/MarkersFinder.R,sha256=mEhdih69dRxjCqTQ2i75fJ1ZpPzI4i7mcQcgM-e86dI,4679
|
|
101
103
|
biopipen/scripts/scrna/SCImpute.R,sha256=dSJOHhmJ3x_72LBRXT72dbCti5oiB85CJ-OjWtqONbk,2958
|
|
102
104
|
biopipen/scripts/scrna/ScFGSEA.R,sha256=gnh2HzPTzBkL8L15MuO7bTMQHlsSKhXiJws8TvfreNE,4492
|
|
103
105
|
biopipen/scripts/scrna/SeuratClusterStats.R,sha256=Ub6KhbWR2-p6XXY9ekrFOGP9f-Q4MpOulwtq7kJS6UM,14656
|
|
@@ -115,6 +117,9 @@ biopipen/scripts/scrna_metabolic_landscape/MetabolicFeatures.R,sha256=THm07CLSq8
|
|
|
115
117
|
biopipen/scripts/scrna_metabolic_landscape/MetabolicFeaturesIntraSubsets.R,sha256=mPHAAG8qHa0uHN3EoMJqwhxsPKfCuIhRx2ahnn2NwSc,3570
|
|
116
118
|
biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayActivity.R,sha256=2DOUVy6mRXVBHFj4g65zJ73mCb_JECU_QM-lLdVwB9A,12083
|
|
117
119
|
biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.R,sha256=8hOG6FsOViXiMormMTa4tqiL9rPDUYHBnu9FdGI1tgM,7930
|
|
120
|
+
biopipen/scripts/tcgamaf/Maf2Vcf.py,sha256=MGc-viCLvfmbLbW7Kc4pN13FdWXIbCkpVc1bSQwb_ek,672
|
|
121
|
+
biopipen/scripts/tcgamaf/MafAddChr.py,sha256=V10HMisl12O3ZfXuRmFNdy5p-3mr43WCvy0GHxSpwfA,494
|
|
122
|
+
biopipen/scripts/tcgamaf/maf2vcf.pl,sha256=hJKcH-NbgWK6fmK7f3qex7ozJJl-PqCNPXqpwfcHwJg,22707
|
|
118
123
|
biopipen/scripts/tcr/Attach2Seurat.R,sha256=kJck_jpjpLhUx1_9vjBeKWCrzI8Gb09nGwUOtp1Ztnk,1315
|
|
119
124
|
biopipen/scripts/tcr/CloneResidency.R,sha256=Xl6kytB1ebIay0ioms1cBwWS_ayhV31U3MPY0fm2xMc,9331
|
|
120
125
|
biopipen/scripts/tcr/CloneSizeQQPlot.R,sha256=5FPfWQjxTsv59KSDQaDWj3C95zPQMngKG7qOf95NEzI,4527
|
|
@@ -132,10 +137,11 @@ biopipen/scripts/vcf/TruvariBench.sh,sha256=80yLQ73OzSgsJ4ltzgpcWxYvvX1hFnCG8YSB
|
|
|
132
137
|
biopipen/scripts/vcf/TruvariBenchSummary.R,sha256=YlcD9qLtK3aeW3XeLx8pXTe7yOkbaYJyLHb2TYijm8A,1474
|
|
133
138
|
biopipen/scripts/vcf/TruvariConsistency.R,sha256=dqoLHCzCeyJ3JWyDX8Q8MzIFwkVK8Jg71Ml45d96Cxg,2293
|
|
134
139
|
biopipen/scripts/vcf/Vcf2Bed.py,sha256=LzyJ9qW1s5mbfF8maLc77_0rE98KMc2lq1R94_NFbSU,855
|
|
140
|
+
biopipen/scripts/vcf/VcfAnno.py,sha256=2Ry3lFTJN9ohDat4O6ZOtTcBLBgS6jvthx13SFhL7RY,734
|
|
135
141
|
biopipen/scripts/vcf/VcfDownSample.sh,sha256=yBlyoA8xyHPkVc1XAs1biNZmN7rDR-CMz8qVh2GGvuk,939
|
|
136
142
|
biopipen/scripts/vcf/VcfFilter.py,sha256=0clQi9XuN0B33xAquQ3e7ce1PZlzIOmOFctNA-dpdEw,1881
|
|
137
143
|
biopipen/scripts/vcf/VcfFix.py,sha256=r2bgwwb2hAMr42wjpFZSFcUDxGllvhkOaRY_r9sKLNE,1304
|
|
138
|
-
biopipen/scripts/vcf/VcfFix_utils.py,sha256=
|
|
144
|
+
biopipen/scripts/vcf/VcfFix_utils.py,sha256=Ev_rvgLY9GF-aNntWbjXbl6eVlubw5uyHUD-g1c6Rno,2294
|
|
139
145
|
biopipen/scripts/vcf/VcfIndex.py,sha256=1o18IY9BKb8CYUy8MXMRC4y_6yqg8BL5DTZ8VBxgy4Y,557
|
|
140
146
|
biopipen/scripts/vcf/VcfIntersect.py,sha256=Bola-A_OnhpA9CKUuoJ--ijG70J55Fr9xpcNY3Ymgso,808
|
|
141
147
|
biopipen/scripts/vcf/VcfLiftOver.sh,sha256=NGlLpJRcwenhbm6jmpgxK6k8VtiERNnNe7uLV6cywGc,562
|
|
@@ -151,7 +157,7 @@ biopipen/utils/plot.R,sha256=pzl37PomNeUZPxohHZ2w93j3Fc4T0Qrc62FF-9MTKdw,4417
|
|
|
151
157
|
biopipen/utils/reference.py,sha256=-BuyiugHzy8A-JsnE7umZCJuLEJle7_oDPK0ROleoMU,3465
|
|
152
158
|
biopipen/utils/rnaseq.R,sha256=Ro2B2dG-Z2oVaT5tkwp9RHBz4dp_RF-JcizlM5GYXFs,1298
|
|
153
159
|
biopipen/utils/vcf.py,sha256=ajXs0M_QghEctlvUlSRjWQIABVF02wPdYd-0LP4mIsU,9377
|
|
154
|
-
biopipen-0.
|
|
155
|
-
biopipen-0.
|
|
156
|
-
biopipen-0.
|
|
157
|
-
biopipen-0.
|
|
160
|
+
biopipen-0.8.0.dist-info/METADATA,sha256=uuLnWt_OyAoDPZvIXwKAfmw1n1OWQjAFKWjYZjpMCoA,839
|
|
161
|
+
biopipen-0.8.0.dist-info/WHEEL,sha256=kLuE8m1WYU0Ig0_YEGrXyTtiJvKPpLpDEiChiNyei5Y,88
|
|
162
|
+
biopipen-0.8.0.dist-info/entry_points.txt,sha256=32HZbG--GdGnCHiTeBUiQ0_NkZGshITTOPE1a83-jQc,487
|
|
163
|
+
biopipen-0.8.0.dist-info/RECORD,,
|
|
@@ -12,7 +12,8 @@ misc=biopipen.ns.misc
|
|
|
12
12
|
plot=biopipen.ns.plot
|
|
13
13
|
rnaseq=biopipen.ns.rnaseq
|
|
14
14
|
scrna=biopipen.ns.scrna
|
|
15
|
-
|
|
15
|
+
scrna_metabolic_landscape=biopipen.ns.scrna_metabolic_landscape
|
|
16
|
+
tcgamaf=biopipen.ns.tcgamaf
|
|
16
17
|
tcr=biopipen.ns.tcr
|
|
17
18
|
vcf=biopipen.ns.vcf
|
|
18
19
|
web=biopipen.ns.web
|