biopipen 0.29.0__py3-none-any.whl → 0.29.2__py3-none-any.whl

biopipen/scripts/stats/Mediation.R

@@ -0,0 +1,106 @@
+source("{{biopipen_dir}}/utils/misc.R")
+
+library(rlang)
+library(parallel)
+library(mediation)
+
+infile <- {{in.infile | r}}
+fmlfile <- {{in.fmlfile | r}}
+outfile <- {{out.outfile | r}}
+
+ncores <- {{envs.ncores | r}}
+sims <- {{envs.sims | r}}
+args <- {{envs.args | r}}
+padj <- {{envs.padj | r}}
+cases <- {{envs.cases | r}}
+transpose_input <- {{envs.transpose_input | r}}
+
+set.seed(123)
+
+log_info("Reading input file ...")
+indata <- read.table(infile, header = TRUE, sep = "\t", row.names = NULL, check.names = FALSE)
+if (transpose_input) { indata <- t(indata) }
+
+log_info("Reading formula file/cases ...")
+if (!is.null(fmlfile)) {
+    if (!is.null(cases) && length(cases) > 0) {
+        log_warn("envs.cases ignored as in.fmlfile is provided")
+    }
+    fmldata <- read.table(fmlfile, header = TRUE, sep = "\t", row.names = NULL)
+    # Case   M   Y   X   Cov     Model_M    Model_Y
+    cases <- split(fmldata, fmldata$Case)
+} else if (is.null(cases) || length(cases) == 0) {
+    stop("Either envs.cases or in.fmlfile must be provided")
+}
+
+args <- args %||% list()
+
+medanalysis <- function(i, total) {
+    casename <- names(cases)[i]
+    case <- cases[[casename]]
+    if (total < 50) {
+        log_info("- Case: ", casename)
+    } else if (total < 500) {
+        if (i %% 10 == 0) {
+            log_info("- Processing case {i}/{total} ...")
+        }
+    } else {
+        if (i %% 100 == 0) {
+            log_info("- Processing case {i}/{total} ...")
+        }
+    }
+    M <- case$M
+    Y <- case$Y
+    X <- case$X
+    covs <- case$Cov
+    modelm <- match.fun(case$Model_M)
+    modely <- match.fun(case$Model_Y)
+    fmlm <- as.formula(sprintf("%s ~ %s", bQuote(M), bQuote(X)))
+    fmly <- as.formula(sprintf("%s ~ %s + %s", bQuote(Y), bQuote(M), bQuote(X)))
+    if (!is.null(covs) && length(covs) == 1) {
+        covs <- trimws(strsplit(covs, ",")[[1]])
+    }
+    if (!is.null(covs)) {
+        cov_fml <- as.formula(sprintf("~ . + %s", paste(bQuote(covs), collapse = " + ")))
+        fmlm <- update.formula(fmlm, cov_fml)
+        fmly <- update.formula(fmly, cov_fml)
+    }
+
+    margs <- args
+    args$sims <- sims
+    args$model.m <- modelm(fmlm, data = indata)
+    args$model.y <- modely(fmly, data = indata)
+    args$treat <- X
+    args$mediator <- M
+    args$outcome <- Y
+    if (!is.null(covs)) {
+        args$covariates <- indata[, covs, drop = FALSE]
+    }
+    med <- do_call(mediate, args)
+    if (is.na(med$d1.p) || is.na(med$n1)) {
+        NULL
+    } else {
+        data.frame(
+            Case         = casename,
+            M            = M,
+            X            = X,
+            Y            = Y,
+            ACME         = med$d1,
+            ACME95CI1    = med$d1.ci[1],
+            ACME95CI2    = med$d1.ci[2],
+            TotalEffect  = med$tau.coef,
+            ADE          = med$z1,
+            PropMediated = med$n1,
+            Pval         = med$d1.p
+        )
+    }
+}
+
+total <- length(cases)
+out <- do_call(rbind, mclapply(1:total, medanalysis, total = total, mc.cores = ncores))
+
+if (padj != "none") {
+    out$Padj <- p.adjust(out$Pval, method = padj)
+}
+
+write.table(out, file = outfile, sep = "\t", quote = FALSE, row.names = FALSE)

{biopipen-0.29.0.dist-info → biopipen-0.29.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.29.0
+Version: 0.29.2
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

{biopipen-0.29.0.dist-info → biopipen-0.29.2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biopipen/__init__.py,sha256=RvbohpnoJRSLAwJOFoWTtu5c5Vpi5vWAfsKR12hwJVI,23
+biopipen/__init__.py,sha256=f5--I8wu8KDVcUAUM1dKof58bj59kV6atq2ccm3sqPs,23
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
 biopipen/core/config.toml,sha256=IL31RfhuF-6V46lvLs1F-Z4SPmUuTvWzk5PN37Xjrqc,1907
@@ -18,13 +18,13 @@ biopipen/ns/delim.py,sha256=fejsh4KW1TG5oMZzAC238LvQhBz7brXkfl3BHfnLK5M,5612
 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=PWPJg1Tly465drYxKMbfrFL4waWNrDG0plgYZeEA7Po,11972
-biopipen/ns/regulation.py,sha256=3esve77YuB-vYNoxYZl15GAd3HELX8FauBcrA2X3-mM,11750
+biopipen/ns/plot.py,sha256=r0n10N9iipZgbDZzkJVq4-9drMtinGK0ntBa3Lk2JFc,15771
+biopipen/ns/regulatory.py,sha256=qvc9QrwgwCI_lg0DQ2QOZbAhC8BAD1qnQXSGtAGlVcY,11750
 biopipen/ns/rnaseq.py,sha256=bKAa6friFWof4yDTWZQahm1MS-lrdetO1GqDKdfxXYc,7708
-biopipen/ns/scrna.py,sha256=XQxdHDZjSt0TWTu-6mshYOmPwPg9a86siaYngBku90s,106954
+biopipen/ns/scrna.py,sha256=0MG0uyyrlSfjS-Lp2Abm_4f4LnLwyjUd6mIOtaQv36Q,108085
 biopipen/ns/scrna_metabolic_landscape.py,sha256=6AhaynGG3lNRi96N2tReVT46BJMuEwooSSd2irBoN80,28347
 biopipen/ns/snp.py,sha256=-Jx5Hsv_7KV7TqLU0nHCaPkMEN0CFdi4tNVlyq0rUZ4,27259
-biopipen/ns/stats.py,sha256=57UF9keLEGxg49R9C2Omx0WIXkPSHvLNxGxO3Xzap2M,16568
+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=0aKH_YSLy_-JzV-_VZb0EoScv7JKGrDU7BaeWHjDuRo,22699
@@ -105,7 +105,7 @@ biopipen/scripts/cnvkit/CNVkitScatter.py,sha256=7DhTiXPHEHbdXn0VFcDOR-wTP6sks08N
 biopipen/scripts/cnvkit/CNVkitSegment.py,sha256=q5iGAjY6-yIehPcJpi3hX6EuGre0YgWTPkG_d5LEV48,1629
 biopipen/scripts/cnvkit/guess_baits.py,sha256=7OCMtSMHIJWWZv9qEYVXnB0N4hU_JaGEesKdkr6tvJc,10586
 biopipen/scripts/delim/RowsBinder.R,sha256=yp960u7Ui_jFCL8WDvODa-0vhJvyLo64ll35PzXYUbI,1444
-biopipen/scripts/delim/SampleInfo.R,sha256=1EYlqoVpIEl9l2eBaCLETuI_Ma3HjihS9tRbGmOPiBk,6397
+biopipen/scripts/delim/SampleInfo.R,sha256=5NWYMIgeXjIwmIF-CTifUVyMLiy6RY_6xOMk2iG4v4E,6684
 biopipen/scripts/gene/GeneNameConversion.R,sha256=uAnueB1poicYpQHjUnl4ZBFn3sAWzP9HzmBC7zjlehI,1776
 biopipen/scripts/gene/GenePromoters.R,sha256=0ukq3-wpN6uq_cyJlQvKDVvy0Dv8cI5Htd9t2xpkEyk,2021
 biopipen/scripts/gsea/Enrichr.R,sha256=tr4vInlVIeiGXumh22ARuTQmy0-Qq869RiX7d7ERqCg,661
@@ -116,16 +116,16 @@ biopipen/scripts/misc/Config2File.py,sha256=NUio0uOEuZtUBpuByDSItYu9Kwu5mosb4pdP
 biopipen/scripts/misc/Shell.sh,sha256=Rg8_DOfDFeUjZ_1_EVm2lbzyMLqcEv9A3k6SsTcfZZ0,493
 biopipen/scripts/misc/Str2File.py,sha256=99oQNxChxChNJ9vmD77b48cu-r_P_heSpx7A5wi3qTE,212
 biopipen/scripts/plot/Heatmap.R,sha256=4v_oRME8ZiwczIlBIp-OP_YPWLAvBKzbHiwNBCZ0Xog,1982
-biopipen/scripts/plot/Manhattan.R,sha256=14qWI4l4AgaEys59dI6nigZacQL_QAV9Hm4TVy_rlNY,4529
-biopipen/scripts/plot/QQPlot.R,sha256=qIvMzy3y1JIwsZDr-IlUxO4AexyakqYaMBNohIUv0i4,1678
+biopipen/scripts/plot/Manhattan.R,sha256=QJhJ80d0RycRt26zJXDqkuCh88YW5IkD-8Di2lGSeu8,4732
+biopipen/scripts/plot/QQPlot.R,sha256=HHGBEJKwHz0ZsYdmAebwov9gQuf6taaLTRkeO7KJ8Lw,4094
 biopipen/scripts/plot/ROC.R,sha256=Cr-mHQx6c748fQYkOWO2xIKWwiVAUxGuxn6lYEhNH78,2430
 biopipen/scripts/plot/VennDiagram.R,sha256=GVc-kyHqnXrbXZvy-evcxI1XGtlLSChBiVnMjPywNMA,731
-biopipen/scripts/regulation/MotifAffinityTest.R,sha256=DcetElFSlurIRuOw1YLPvoOPDCnfq-EpgV-e1aKX_nM,8969
-biopipen/scripts/regulation/MotifAffinityTest_AtSNP.R,sha256=SAyTm2-6g5qVJFRrLxEY0QJrLWTkwDi_J_9J7HhtTN8,4438
-biopipen/scripts/regulation/MotifAffinityTest_MotifBreakR.R,sha256=wCK4tLx1iWh_OwW7ZvLTCjTGWCIfVqw-lYC0-JqIPqg,3338
-biopipen/scripts/regulation/MotifScan.py,sha256=nxwfDV3sXWk62x0WFpzxEZuUjJSErZvYkB2KJP7uAnc,5336
-biopipen/scripts/regulation/atSNP.R,sha256=TXJARbE0rDIzSq6Spacz_HsM_DXdREJ95ZsBg26trgw,1288
-biopipen/scripts/regulation/motifBreakR.R,sha256=trzvvTvwc5gSO427wkqx93FecuQxLGa9kNqodKa8S0U,70236
+biopipen/scripts/regulatory/MotifAffinityTest.R,sha256=eeBauaAfyEcOIznoXRRWXeRUvAd0waU0R5CCzwQ8kgs,8969
+biopipen/scripts/regulatory/MotifAffinityTest_AtSNP.R,sha256=SAyTm2-6g5qVJFRrLxEY0QJrLWTkwDi_J_9J7HhtTN8,4438
+biopipen/scripts/regulatory/MotifAffinityTest_MotifBreakR.R,sha256=wCK4tLx1iWh_OwW7ZvLTCjTGWCIfVqw-lYC0-JqIPqg,3338
+biopipen/scripts/regulatory/MotifScan.py,sha256=WtSbs8z08oeTgzjr0LfIDmjbUdknAh1raa_QPQ_NCFg,5336
+biopipen/scripts/regulatory/atSNP.R,sha256=TXJARbE0rDIzSq6Spacz_HsM_DXdREJ95ZsBg26trgw,1288
+biopipen/scripts/regulatory/motifBreakR.R,sha256=trzvvTvwc5gSO427wkqx93FecuQxLGa9kNqodKa8S0U,70236
 biopipen/scripts/rnaseq/Simulation-ESCO.R,sha256=68cEHDdJclX8P8Q7ey9yBOfK09M_kxlL6zgYXsEL2Rs,6378
 biopipen/scripts/rnaseq/Simulation-RUVcorr.R,sha256=6C6Ke5RLF0fC2V9WQPoFEdqoDabCnhslZBIyB6zhIxc,1155
 biopipen/scripts/rnaseq/Simulation.R,sha256=PNEDUwEEOMGwgNyx5VPDAbzSLS74gqAxKenv5Uw_8zo,850
@@ -143,25 +143,25 @@ biopipen/scripts/scrna/ExprImputation-alra.R,sha256=w3W1txJcdWg52-SETY2Z0lO7maDN
 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=-rQyu0uXJscQbRUH6XDPxIFawOwqDxch75yyG1ArMaU,22670
-biopipen/scripts/scrna/MetaMarkers.R,sha256=9ve1X0TrDzS_ZEW6HtU3n8R-uPx7q-hYMMNFVDSE8wQ,11272
+biopipen/scripts/scrna/MarkersFinder.R,sha256=6CjciBZsVUIjsEe_xpO0s5K-uy2kKa1c76Ks_lndX-g,22950
+biopipen/scripts/scrna/MetaMarkers.R,sha256=xb1dt4N-ra26l6pWmL4Ieix0MB6QOU7CDcxufMZE3Xk,12064
 biopipen/scripts/scrna/ModuleScoreCalculator.R,sha256=JSHd-_-KiFqW8avCGxgU4T-C5BtDr2u0kwIvEu2lFIg,4188
 biopipen/scripts/scrna/RadarPlots.R,sha256=TGPUTUcHOHgd9rsNtLYT-N6WHiFNDBZsiIoqkyAJh0A,13020
 biopipen/scripts/scrna/SCImpute.R,sha256=dSJOHhmJ3x_72LBRXT72dbCti5oiB85CJ-OjWtqONbk,2958
 biopipen/scripts/scrna/ScFGSEA.R,sha256=2UCTCIydVkPGvn7WP-_fcE7857iKKDxY56-j-ruyO8o,6254
 biopipen/scripts/scrna/Seurat2AnnData.R,sha256=qz4u-B5J3GMwttubnNnByJXreziFbrP5Mak0L0q7eG0,1557
 biopipen/scripts/scrna/SeuratClusterStats-dimplots.R,sha256=gViDgQ8NorYD64iK0FgcODOrDOw0tExZmhuPRuLNp4g,2354
-biopipen/scripts/scrna/SeuratClusterStats-features.R,sha256=W7iYhaFsC5EMZLO50QukYPLYGK4bq9kQc1VT5FwvI68,15496
+biopipen/scripts/scrna/SeuratClusterStats-features.R,sha256=Cg7fVdDnapS98ak9z2Ha77CLqBkNJ4IYX1q1ssfGNeU,15599
 biopipen/scripts/scrna/SeuratClusterStats-hists.R,sha256=YhuD-GePjJPSkR0iLRgV_hiGHD_bnOIKp-LB6GCwquo,5037
 biopipen/scripts/scrna/SeuratClusterStats-ngenes.R,sha256=GVKIXFNS_syCuSN8oxoBkjxxAeI5LdSxh-qLVkUsbDA,2146
 biopipen/scripts/scrna/SeuratClusterStats-stats.R,sha256=bBbvNCvV6dZLg9zvhh2nR48_53md5A5UEqrPXD00MZU,9263
 biopipen/scripts/scrna/SeuratClusterStats.R,sha256=ouWoj7Q644uG3MUlT23AES8f74g38-jPtPhINSvoUas,1267
-biopipen/scripts/scrna/SeuratClustering.R,sha256=xumBiqNnXcOn50tRmcqev9EBRUvf-ck9rEpAWeDXToE,7530
+biopipen/scripts/scrna/SeuratClustering.R,sha256=VOpJfICDrEIh9ATss8RJYOvsoLJLxaidg4F0aqOYfp0,7893
 biopipen/scripts/scrna/SeuratFilter.R,sha256=BrYK0MLdaTtQvInMaQsmOt7oH_hlks0M1zykkJtg2lM,509
 biopipen/scripts/scrna/SeuratLoading.R,sha256=ekWKnHIqtQb3kHVQiVymAHXXqiUxs6KKefjZKjaykmk,900
 biopipen/scripts/scrna/SeuratMap2Ref.R,sha256=qnFkOCudqC-j5uAszBssWM9Xg_vO3H9_Hj0n5wdOmBc,9757
 biopipen/scripts/scrna/SeuratMetadataMutater.R,sha256=Pp4GsF3hZ6ZC2vroC3LSBmVa4B1p2L3hbh981yaAIeQ,1093
-biopipen/scripts/scrna/SeuratPreparing.R,sha256=t6GOcc9ZNwpRLeES7uBWja9RF6u6k5I_TXcdK4Ve7d0,18683
+biopipen/scripts/scrna/SeuratPreparing.R,sha256=nC7wPwS-s0ZGVV1vV50PvFewTirmRsiozT1C07pGHpE,22532
 biopipen/scripts/scrna/SeuratSplit.R,sha256=vdK11V39_Uo_NaOh76QWCtxObGaEr5Ynxqq0hTiSvsU,754
 biopipen/scripts/scrna/SeuratSubClustering.R,sha256=ooEQhUneYvSiRcwlqC9Mc8WE0g5pLEtKtQWYrKN3cck,8001
 biopipen/scripts/scrna/SeuratSubset.R,sha256=yVA11NVE2FSSw-DhxQcJRapns0tNNHdyDYi5epO6SKM,1776
@@ -170,11 +170,11 @@ biopipen/scripts/scrna/Subset10X.R,sha256=T2nJBTwOe12AIKC2FZsMSv6xx3s-67CYZokpz5
 biopipen/scripts/scrna/TopExpressingGenes.R,sha256=kXMCYHVytgVgO_Uq66fKKFCFV2PPXE8VREy_0yYPLpU,7475
 biopipen/scripts/scrna/celltypist-wrapper.py,sha256=f5M8f4rU5nC7l17RS0YVmUPpLLz4D6PIcgWtA77UExM,1722
 biopipen/scripts/scrna/sctype.R,sha256=NaUJkABwF5G1UVm1CCtcMbwLSj94Mo24mbYCKFqo1Bw,6524
-biopipen/scripts/scrna_metabolic_landscape/MetabolicFeatures.R,sha256=sOnHSH0Ld-tXSIXJPnXLYgRtEru5M0g3HRxbrHWQ_0U,5170
-biopipen/scripts/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.R,sha256=RPSxEHWk50Fyw5YPBVVGeWwd55Hi0zjbipLuM5O4tjs,5465
+biopipen/scripts/scrna_metabolic_landscape/MetabolicFeatures.R,sha256=EFUhI65cPEktZnZquzfVoJcBd_pNcT5jag5XOWHj-Os,5222
+biopipen/scripts/scrna_metabolic_landscape/MetabolicFeaturesIntraSubset.R,sha256=jeTuhWEn2ajL1ZmGpCBy7cBSd1d387P-YetnB6qjhxc,5502
 biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayActivity.R,sha256=95DLX1Rz0tobOuDZ8V9YdGgO0KiNthhccoeeOK21tno,16216
 biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.R,sha256=rQ9iwGh9FNRZlJJzM4QItdyXmebfzLAq05ZAjb1kGUw,9831
-biopipen/scripts/snp/MatrixEQTL.R,sha256=Wr1m4RLcxisJgy5_7Tp_SoOoDZIBfRjHuUVnYLBWtAo,7186
+biopipen/scripts/snp/MatrixEQTL.R,sha256=QPnUW7Rk5UrAQLiBg9FdCItUC26RDBHf7UrfL66dMto,7202
 biopipen/scripts/snp/Plink2GTMat.py,sha256=ypxuT6YEBuuSk9TML9SHhVtA38GlZvB-3tQakJd8YLQ,5052
 biopipen/scripts/snp/PlinkCallRate.R,sha256=lkx93TyZjnvOWuq7W5zvdIlYmTC4n4ys52VymA7PvPM,6160
 biopipen/scripts/snp/PlinkFilter.py,sha256=eqC18ne3rPUzIJ_KjqvwQ79MyeMxe0oh4S9PnhfhK1E,3200
@@ -182,12 +182,13 @@ biopipen/scripts/snp/PlinkFreq.R,sha256=Y8R-jE4upWe6B4yf7G9BCjEyv6HXItHOaUQzVInX
 biopipen/scripts/snp/PlinkFromVcf.py,sha256=TZaJ117Qp-gbqPX7WK6r7Zw8XHVXbRO6wb0V1NQouxw,2284
 biopipen/scripts/snp/PlinkHWE.R,sha256=Ncs4ctTDCnfGxs5HbyNxsNuq3Cn_Dwo1iFKdbj6GJSc,2201
 biopipen/scripts/snp/PlinkHet.R,sha256=r35hzA3A5lrqJN1kWxd2bYucTZd1eNd_vDjqhprur34,3005
-biopipen/scripts/snp/PlinkIBD.R,sha256=DJjmcwWYso8pY6HTKXLEIWsTurctknQxOQScG_ikBck,5640
+biopipen/scripts/snp/PlinkIBD.R,sha256=5y2C6UnMyIGrdiSpHYd63r8vGbAiMTLI4XDA82mur7Y,5712
 biopipen/scripts/snp/PlinkSimulation.py,sha256=mSSoGGG6sbEPBcUGdHgbebUrg4DiHeyNyc7jLPjV5pY,4169
 biopipen/scripts/snp/PlinkUpdateName.py,sha256=sYyb0ek46wRQfclFfoJEhQyQ-zWsFd2xpFHKw3jbsq4,4055
 biopipen/scripts/stats/ChowTest.R,sha256=4p7NULmfOZSfeBSQ04els0h3cXOK5yeCJJ4-gEBPOGk,3617
 biopipen/scripts/stats/DiffCoexpr.R,sha256=5hQDV2_7bKdKUsOGMZUa0GS5rc7kFspxonNyFEPmtbc,4516
 biopipen/scripts/stats/LiquidAssoc.R,sha256=s-XJbFoOfH4eWSkxbbOSHZ1x16lY0Sdod_V1KvSkM8k,3727
+biopipen/scripts/stats/Mediation.R,sha256=jf7ORVbbd9wtEOEJRLowKexQCkOhFmc4v5kkPsNqWpY,3160
 biopipen/scripts/stats/MetaPvalue.R,sha256=fnqayZeHd61cP9PxZZAebg5lE7JQgFG5MElCct43S1M,4012
 biopipen/scripts/stats/MetaPvalue1.R,sha256=falhaOeoa8E7ZbddXfGsSdim5P7eQvA7RFGD7XSrBUk,1733
 biopipen/scripts/tcgamaf/Maf2Vcf.py,sha256=Cxh7fiSNCxWDTfIJqZDOOnaSrw-85S_fH2U-PWY03hc,704
@@ -268,7 +269,7 @@ biopipen/utils/reference.py,sha256=oi5evicLwHxF0KAIPNZohBeHJLJQNWFJH0cr2y5pgcg,5
 biopipen/utils/rnaseq.R,sha256=Ro2B2dG-Z2oVaT5tkwp9RHBz4dp_RF-JcizlM5GYXFs,1298
 biopipen/utils/single_cell.R,sha256=pJjYP8bIZpNAtTQ32rOXhZxaM1Y-6D-xUcK3pql9tbk,4316
 biopipen/utils/vcf.py,sha256=ajXs0M_QghEctlvUlSRjWQIABVF02wPdYd-0LP4mIsU,9377
-biopipen-0.29.0.dist-info/METADATA,sha256=dQ6UcVOLcX89F69jLAtXIczJo77lhkrSDdE5QrBgIJg,882
-biopipen-0.29.0.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-biopipen-0.29.0.dist-info/entry_points.txt,sha256=99uvED4sthSUVArFUMdMNLbYkVIEDLPUYg92JB22lt8,625
-biopipen-0.29.0.dist-info/RECORD,,
+biopipen-0.29.2.dist-info/METADATA,sha256=9tT8IW-AiQXwRLIzbARle_vaYVL7h5f_wyEwq8ZAHA8,882
+biopipen-0.29.2.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+biopipen-0.29.2.dist-info/entry_points.txt,sha256=69SbeMaF47Z2DS40yo-qDyoBKmMmumrNnsjEZMOioCE,625
+biopipen-0.29.2.dist-info/RECORD,,

{biopipen-0.29.0.dist-info → biopipen-0.29.2.dist-info}/entry_points.txt

@@ -11,7 +11,7 @@ gene=biopipen.ns.gene
 gsea=biopipen.ns.gsea
 misc=biopipen.ns.misc
 plot=biopipen.ns.plot
-regulation=biopipen.ns.regulation
+regulatory=biopipen.ns.regulatory
 rnaseq=biopipen.ns.rnaseq
 scrna=biopipen.ns.scrna
 scrna_metabolic_landscape=biopipen.ns.scrna_metabolic_landscape