biopipen 0.34.8__py3-none-any.whl → 0.34.10__py3-none-any.whl

biopipen/__init__.py

@@ -1 +1 @@
-__version__ = "0.34.8"
+__version__ = "0.34.10"

biopipen/ns/regulatory.py

@@ -132,6 +132,9 @@ class MotifAffinityTest(Proc):
             If no `regulator_col` is provided, no regulator information is written in
             the output. Otherwise, the regulator information is written in the output in
             the `Regulator` column.
+        var_col: The column names in the `in.motiffile` containing the variant information.
+            It has to be matching the names in the `in.varfile`. This is helpful when
+            we only need to test the pairs of variants and motifs in the `in.motiffile`.
         notfound (choice): What to do if a motif is not found in the database,
             or a regulator is not found in the regulator-motif mapping (envs.regmotifs)
             file.
@@ -200,6 +203,7 @@ class MotifAffinityTest(Proc):
         "bcftools": config.exe.bcftools,
         "motif_col": None,
         "regulator_col": None,
+        "var_col": None,
         "notfound": "error",
         "motifdb": config.ref.tf_motifdb,
         "regmotifs": config.ref.tf_motifs,

biopipen/ns/scrna.py

@@ -118,6 +118,10 @@ class SeuratPreparing(Proc):
             It doesn't work when data is loaded from loom files.
         cell_qc: Filter expression to filter cells, using
             `tidyrseurat::filter()`.
+            It can also be a dictionary of expressions, where the names of the list are
+            sample names.
+            You can have a default expression in the list with the name "DEFAULT" for
+            the samples that are not listed.
             Available QC keys include `nFeature_RNA`, `nCount_RNA`,
             `percent.mt`, `percent.ribo`, `percent.hb`, and `percent.plat`.
 
@@ -782,11 +786,16 @@ class ModuleScoreCalculator(Proc):
             will perform diffusion map as a reduction and add the first 2
             components as `DC_1` and `DC_2` to the metadata. `diffmap` is a shortcut
             for `diffusion_map`. Other key-value pairs will pass to
-            [`destiny::DiffusionMap()`](https://www.rdocumentation.org/packages/destiny/versions/2.0.4/topics/DiffusionMap%20class).
+            [`destiny::DiffusionMap()`](https://www.rdocumentation.org/packages/destiny/versions/2.0.4/topics/DiffusionMap class).
             You can later plot the diffusion map by using
             `reduction = "DC"` in `env.dimplots` in `SeuratClusterStats`.
             This requires [`SingleCellExperiment`](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html)
             and [`destiny`](https://bioconductor.org/packages/release/bioc/html/destiny.html) R packages.
+        post_mutaters (type=json): The mutaters to mutate the metadata after
+            calculating the module scores.
+            The mutaters will be applied in the order specified.
+            This is useful when you want to create new scores based on the
+            calculated module scores.
     """  # noqa: E501
 
     input = "srtobj:file"
@@ -810,6 +819,7 @@ class ModuleScoreCalculator(Proc):
             # "Activation": {"features": "IFNG"},
             # "Proliferation": {"features": "STMN1,TUBB"},
         },
+        "post_mutaters": {},
     }
     script = "file://../scripts/scrna/ModuleScoreCalculator.R"
 
@@ -1131,7 +1141,7 @@ class MarkersFinder(Proc):
                 - res (type=int): The resolution of the plots.
                 - height (type=int): The height of the plots.
                 - width (type=int): The width of the plots.
-            - <more>: See <https://pwwang.github.io/scplotter/reference/EnrichmentPlot.htmll>.
+            - <more>: See <https://pwwang.github.io/scplotter/reference/EnrichmentPlot.html>.
         enrich_plots (type=json): Cases of the plots to generate for the enrichment analysis.
             The keys are the names of the cases and the values are the dicts inherited from `enrich_plots_defaults`.
             The cases under `envs.cases` can inherit this options.
@@ -1781,6 +1791,11 @@ class CellTypeAnnotation(Proc):
             the original cell types will be kept and nothing will be changed.
             ///
 
+        more_cell_types (type=json): The additional cell type annotations to add to the metadata.
+            The keys are the new column names and the values are the cell types lists.
+            The cell type lists work the same as `cell_types` above.
+            This is useful when you want to keep multiple annotations of cell types.
+
         sccatch_args (ns): The arguments for `scCATCH::findmarkergene()` if `tool` is `sccatch`.
             - species: The specie of cells.
             - cancer: If the sample is from cancer tissue, then the cancer type may be defined.
@@ -1842,6 +1857,7 @@ class CellTypeAnnotation(Proc):
         "sctype_tissue": None,
         "sctype_db": config.ref.sctype_db,
         "cell_types": [],
+        "more_cell_types": None,
         "sccatch_args": {
             "species": None,
             "cancer": "Normal",
@@ -2524,6 +2540,10 @@ class CellCellCommunicationPlots(Proc):
         cases (type=json): The cases for the plots.
             The keys are the names of the cases and the values are the arguments for
             the plots. The arguments include the ones inherited from `envs`.
+            You can have a special `plot_type` `"table"` to generate a table for the
+            ccc data to save as a text file and show in the report.
+            If no cases are given, a default case will be used, with the
+            key `Cell-Cell Communication`.
         <more>: Other arguments passed to
             [scplotter::CCCPlot](https://pwwang.github.io/scplotter/reference/CCCPlot.html)
     """  # noqa: E501

biopipen/scripts/regulatory/MotifAffinityTest.R

@@ -14,6 +14,7 @@ bcftools <- {{envs.bcftools | r}}
 genome <- {{envs.genome | r}}
 motif_col <- {{envs.motif_col | r}}
 regulator_col <- {{envs.regulator_col | r}}
+var_col <- {{envs.var_col | r}}
 notfound <- {{envs.notfound | r}}
 motifdb <- {{envs.motifdb | r}}
 regmotifs <- {{envs.regmotifs | r}}
@@ -21,6 +22,7 @@ devpars <- {{envs.devpars | r}}
 plot_nvars <- {{envs.plot_nvars | r}}
 plots <- {{envs.plots | r}}
 cutoff <- {{envs.cutoff | r}}
+set.seed(8525)
 
 if (is.null(motifdb) || !file.exists(motifdb)) {
     stop("Motif database (envs.motifdb) is required and must exist")
@@ -47,10 +49,21 @@ log <- get_logger()
 log$info("Reading input regulator/motif file ...")
 in_motifs <- read.table(motiffile, header=TRUE, sep="\t", stringsAsFactors=FALSE, check.names = FALSE)
 
+
 log$info("Ensuring motifs and regulators in the input data ...")
-in_motifs <- ensure_regulator_motifs(in_motifs, outdir, motif_col, regulator_col, regmotifs, notfound = notfound)
+in_motifs <- ensure_regulator_motifs(in_motifs, outdir, motif_col, regulator_col, var_col, regmotifs, notfound = notfound)
 genome_pkg <- get_genome_pkg(genome)
 
+motif_var_pairs <- NULL
+if (!is.null(var_col)) {
+    log$info("Obtaining motif-variant pairs to test ...")
+    if (!var_col %in% colnames(in_motifs)) {
+        stop("Variant column (envs.var_col) not found in the input motif file")
+    }
+
+    motif_var_pairs <- unique(paste0(in_motifs[[motif_col]], " // ", in_motifs[[var_col]]))
+}
+
 log$info("Reading variant file ...")
 if (grepl("\\.vcf$", varfile) || grepl("\\.vcf\\.gz$", varfile)) {
     log$info("Converting VCF file to BED file ...")
@@ -77,10 +90,13 @@ mdb <- read_meme_to_motifdb(motifdb, in_motifs, motif_col, regulator_col, notfou
 tool <- tolower(tool)
 tool <- match.arg(tool, c("motifbreakr", "atsnp"))
 
-if (tool == "motifbreakr") {
+{% if envs.tool == "motifbreakr" %}
     motifbreakr_args <- {{envs.motifbreakr_args | r}}
     {% include biopipen_dir + "/scripts/regulatory/MotifAffinityTest_MotifBreakR.R" %}
-} else {  # atsnp
-    atsnp_args <- {{envs.atsnp_args | r}}
+{% else %}
+    atsnp_args <- list_update(
+        list(padj_cutoff = TRUE, padj = "BH", p = "Pval_diff"),
+        {{envs.atsnp_args | r}}
+    )
     {% include biopipen_dir + "/scripts/regulatory/MotifAffinityTest_AtSNP.R" %}
-}
+{% endif %}

biopipen/scripts/regulatory/MotifAffinityTest_AtSNP.R

@@ -46,6 +46,13 @@ atsnp_result <- ComputePValues(
     testing.mc = TRUE
 )
 
+if (!is.null(motif_var_pairs)) {
+    log$info("Filtering motif-variant pairs ...")
+    atsnp_result$motifs_vars <- paste0(atsnp_result$motif, " // ", atsnp_result$snpid)
+    atsnp_result <- atsnp_result[atsnp_result$motifs_vars %in% motif_var_pairs, , drop = FALSE]
+    atsnp_result$motifs_vars <- NULL
+}
+
 padj_col <- paste0(atsnp_args$p, "_adj")
 atsnp_result[[padj_col]] <- p.adjust(atsnp_result[[atsnp_args$p]], method = atsnp_args$padj)
 cutoff_col <- if (atsnp_args$padj_cutoff) padj_col else atsnp_args$p
@@ -87,7 +94,8 @@ write.table(
 
 log$info("Plotting variants ...")
 # Convert result to GRanges object
-atsnp_result$alleleDiff <- -atsnp_result[[cutoff_col]]
+atsnp_result$alleleDiff <- -log10(atsnp_result[[cutoff_col]])
+atsnp_result <- atsnp_result[order(-atsnp_result$alleleDiff), , drop = FALSE]
 atsnp_result$effect <- "strong"
 atsnp_result$motifPos <- lapply(atsnp_result$motifPos, function(x) as.integer(unlist(strsplit(x, ","))))
 atsnp_result <- makeGRangesFromDataFrame(atsnp_result, keep.extra.columns = TRUE, starts.in.df.are.0based = TRUE)
@@ -96,7 +104,6 @@ attributes(atsnp_result)$genome.package <- genome_pkg
 attributes(atsnp_result)$motifs <- mdb
 
 if (is.null(plots) || length(plots) == 0) {
-    atsnp_result <- atsnp_result[order(-abs(atsnp_result$alleleDiff)), , drop = FALSE]
     atsnp_result <- atsnp_result[1:min(plot_nvars, length(atsnp_result)), , drop = FALSE]
     variants <- unique(atsnp_result$SNP_id)
 } else {

biopipen/scripts/regulatory/MotifAffinityTest_MotifBreakR.R

@@ -50,6 +50,7 @@ results <- motifbreakR(
 
 log$info("Calculating p values ...")
 results <- calculatePvalue(results)
+results$.id <- 1:length(results)
 results_to_save <- as.data.frame(unname(results))
 results_to_save$motifPos <- lapply(results_to_save$motifPos, function(x) paste(x, collapse = ","))
 results_to_save$altPos <- lapply(results_to_save$altPos, function(x) paste(x, collapse = ","))
@@ -60,20 +61,28 @@ if (!is.null(regulator_col)) {
         drop = TRUE
     ]
 }
-results_to_save <- apply(results_to_save, 2, as.character)
+results_to_save <- as.data.frame(apply(results_to_save, 2, as.character))
+
+if (!is.null(motif_var_pairs)) {
+    log$info("Filtering motif-variant pairs ...")
+    results_to_save$motifs_vars <- paste0(results_to_save$providerId, " // ", results_to_save$SNP_id)
+    results_to_save <- results_to_save[results_to_save$motifs_vars %in% motif_var_pairs, , drop = FALSE]
+    results_to_save$motifs_vars <- NULL
+}
 
 write.table(
     results_to_save,
     file = file.path(outdir, "motifbreakr.txt"),
     sep = "\t", quote = FALSE, row.names = FALSE
 )
-rm(results_to_save)
+# rm(results_to_save)
 
 log$info("Plotting variants ...")
 if (is.null(plots) || length(plots) == 0) {
-    results <- results[order(-abs(results$alleleDiff)), , drop = FALSE]
-    results <- results[1:min(plot_nvars, length(results)), , drop = FALSE]
-    variants <- unique(results$SNP_id)
+    results_to_save$alleleDiff <- as.numeric(results_to_save$alleleDiff)
+    results_to_save <- results_to_save[order(-abs(results_to_save$alleleDiff)), , drop = FALSE]
+    results_to_save <- results_to_save[1:min(plot_nvars, nrow(results_to_save)), , drop = FALSE]
+    variants <- unique(results_to_save$SNP_id)
 } else {
     variants <- names(plots)
 }
@@ -88,7 +97,7 @@ for (variant in variants) {
     if (is.null(plots[[variant]]$devpars)) {
         plots[[variant]]$devpars <- devpars
     }
-    res <- results[results$SNP_id == variant, , drop = FALSE]
+    res <- results[results$SNP_id == variant & results$.id %in% results_to_save$.id, , drop = FALSE]
     res <- subset(res, subset = eval(parse(text = plots[[variant]]$which)))
 
     plot_variant_motifs(res, variant, plots[[variant]]$devpars, outdir)

biopipen/scripts/regulatory/VariantMotifPlot.R

@@ -33,7 +33,7 @@ log$info("Reading input data ...")
 indata <- read.table(infile, header=TRUE, sep="\t", stringsAsFactors=FALSE, check.names = FALSE)
 
 log$info("Ensuring regulators in the input data ...")
-indata <- ensure_regulator_motifs(indata, outdir, motif_col, regulator_col, regmotifs, notfound = notfound)
+indata <- ensure_regulator_motifs(indata, outdir, motif_col, regulator_col, "SNP_id", regmotifs, notfound = notfound)
 genome_pkg <- get_genome_pkg(genome)
 
 log$info("Reading motif database ...")

biopipen/scripts/regulatory/motifs-common.R

@@ -138,12 +138,13 @@ motifdb_to_motiflib <- function(motifdb) {
 #' @param outdir Output directory, used to save un-matched regulators
 #' @param motif_col Column name for the motif
 #' @param regulator_col Column name for the regulator
+#' @param var_col Column name for the variant
 #' @param regmotifs Regulator-motif mapping file
 #' @param log_indent Indentation for log messages
 #' @param notfound Action to take if regulators are not found in the mapping file
 #' @return Data frame with regulators and motifs
 #' @export
-ensure_regulator_motifs <- function (indata, outdir, motif_col, regulator_col, regmotifs, log_indent = "", notfound = "error", log = NULL) {
+ensure_regulator_motifs <- function (indata, outdir, motif_col, regulator_col, var_col, regmotifs, log_indent = "", notfound = "error", log = NULL) {
     if (is.null(motif_col)) {
         if (is.null(regmotifs)) {
             stop("Regulator-motif mapping file (envs.regmotifs) is required when no motif column (envs.motif_col) is provided")
@@ -198,7 +199,7 @@ ensure_regulator_motifs <- function (indata, outdir, motif_col, regulator_col, r
             regulator_col <<- rm_reg_col
         }
     } else {
-        indata <- indata[!duplicated(indata[, c(regulator_col, motif_col), drop = FALSE]), , drop = FALSE]
+        indata <- indata[!duplicated(indata[, c(regulator_col, motif_col, var_col), drop = FALSE]), , drop = FALSE]
     }
 
     return(indata)

biopipen/scripts/scrna/CellCellCommunication.py

@@ -7,6 +7,10 @@ import scanpy
 import liana
 import liana.method.sc._liana_pipe as _liana_pipe
 
+# AttributeError: module 'numpy' has no attribute 'product'
+if not hasattr(np, "product"):
+    np.product = np.prod
+
 # monkey-patch liana.method.sc._liana_pipe._trimean due to the updates by scipy 1.14
 # https://github.com/scipy/scipy/commit/a660202652deead0f3b4b688eb9fdcdf9f74066c
 def _trimean(a, axis=0):

biopipen/scripts/scrna/CellCellCommunicationPlots.R

@@ -27,7 +27,7 @@ defaults <- list(
     devpars = list(res = 100)
 )
 
-cases <- expand_cases(cases, defaults)
+cases <- expand_cases(cases, defaults, default_case = "Cell-Cell Communication")
 log <- get_logger()
 reporter <- get_reporter()
 
@@ -35,12 +35,31 @@ do_case <- function(name) {
     log$info("- Case: {name}")
     case <- cases[[name]]
     info <- case_info(name, outdir, is_dir = FALSE)
-    case <- extract_vars(case, "subset", "devpars", "more_formats", "descr")
+    case <- extract_vars(case, subset_ = "subset", "devpars", "more_formats", "descr")
 
     case$data <- ccc
-    if (!is.null(case$subset)) {
-        case$data <- ccc %>% dplyr::filter(!!parse_expr(case$subset))
+    if (!is.null(subset_)) {
+        case$data <- ccc %>% dplyr::filter(!!parse_expr(subset_))
     }
+
+    if (identical(case$plot_type, "table")) {
+        write.table(
+            case$data,
+            file = paste0(info$prefix, ".txt"),
+            sep = "\t",
+            row.names = FALSE,
+            col.names = TRUE,
+            quote = FALSE
+        )
+        report <- list(
+            kind = "table",
+            data = list(nrows = 100),
+            src = paste0(info$prefix, ".txt")
+        )
+        reporter$add2(report, hs = c(info$section, info$name))
+        return()
+    }
+
     if (is.null(case$magnitude)) {
         case$magnitude <- NULL
     }

biopipen/scripts/scrna/CellTypeAnnotation-direct.R

@@ -5,11 +5,15 @@ outfile <- {{out.outfile | r}}
 celltypes <- {{envs.cell_types | r}}
 newcol <- {{envs.newcol | r}}
 merge_same_labels <- {{envs.merge | r}}
+more_cell_types <- {{envs.more_cell_types | r}}
 
 log <- biopipen.utils::get_logger()
 
 if (is.null(celltypes) || length(celltypes) == 0) {
     log$warn("No cell types are given!")
+    if (!is.null(more_cell_types) && length(more_cell_types) > 0) {
+        log$warn("`envs.celltypes` is not given, won't process `envs.more_cell_types`!")
+    }
 
     if (merge_same_labels) {
         log$warn("Ignoring 'envs.merge' because no cell types are given!")
@@ -25,26 +29,43 @@ if (is.null(celltypes) || length(celltypes) == 0) {
     } else {
         idents <- as.character(unique(idents))
     }
-
-    if (length(celltypes) < length(idents)) {
-        celltypes <- c(celltypes, idents[(length(celltypes) + 1):length(idents)])
-    } else if (length(celltypes) > length(idents)) {
-        celltypes <- celltypes[1:length(idents)]
-        log$warn("The length of cell types is longer than the number of clusters!")
+    process_celltypes <- function(ct, key = NULL) {
+        if (length(ct) < length(idents)) {
+            ct <- c(ct, idents[(length(ct) + 1):length(idents)])
+        } else if (length(ct) > length(idents)) {
+            ct <- ct[1:length(idents)]
+            if (is.null(key)) {
+                log$warn("The length of cell types is longer than the number of clusters!")
+            } else {
+                log$warn(paste0("The length of cell types for '", key, "' is longer than the number of clusters!"))
+            }
+        }
+        for (i in seq_along(ct)) {
+            if (ct[i] == "-" || ct[i] == "") {
+                ct[i] <- idents[i]
+            }
+        }
+        names(ct) <- idents
+        return(ct)
     }
-    for (i in seq_along(celltypes)) {
-        if (celltypes[i] == "-" || celltypes[i] == "") {
-            celltypes[i] <- idents[i]
+
+    if (!is.null(more_cell_types) && length(more_cell_types) > 0) {
+        for (key in names(more_cell_types)) {
+            ct <- more_cell_types[[key]]
+            ct <- process_celltypes(ct, key)
+            log$info(paste0("Adding additional cell type annotation: '", key, "' ..."))
+            sobj@meta.data[[key]] <- ct[as.character(Idents(sobj))]
         }
     }
-    names(celltypes) <- idents
+
+    celltypes <- process_celltypes(celltypes)
 
     log$info("Renaming cell types ...")
     if (is.null(newcol)) {
         has_na <- "NA" %in% unlist(celltypes) || anyNA(unlist(celltypes))
         sobj$seurat_clusters_id <- Idents(sobj)
         celltypes$object <- sobj
-        sobj <- do_call(RenameIdents, celltypes)
+        sobj <- biopipen.utils::do_call(RenameIdents, celltypes)
         sobj$seurat_clusters <- Idents(sobj)
         if (has_na) {
             log$info("Filtering clusters if NA ...")
@@ -65,5 +86,6 @@ if (is.null(celltypes) || length(celltypes) == 0) {
         sobj <- merge_clusters_with_same_labels(sobj, newcol)
     }
 
+    log$info("Saving Seurat object ...")
     biopipen.utils::save_obj(sobj, outfile)
 }

biopipen/scripts/scrna/MarkersFinder.R

@@ -353,16 +353,24 @@ process_markers <- function(markers, info, case) {
                 for (db in case$dbs) {
                     plots <- list()
                     for (plotname in names(case$enrich_plots)) {
-                        plotargs <- case$enrich_plots[[plotname]]
+                        plotargs <- extract_vars(case$enrich_plots[[plotname]], "descr", allow_nonexisting = TRUE)
                         plotargs$data <- enrich[enrich$Database == db, , drop = FALSE]
 
                         p <- do_call(VizEnrichment, plotargs)
 
                         if (plotargs$plot_type == "bar") {
                             attr(p, "height") <- attr(p, "height") / 1.5
+                            descr <- descr %||% glue::glue(
+                                "The bar plot shows the top enriched terms in database '{db}', ",
+                                "the x-axis shows the -log10 of the adjusted p-values, ",
+                                "and the y-axis shows the term names. The number next to each bar indicates the overlap gene count."
+                            )
                         }
                         outprefix <- file.path(info$prefix, paste0("enrich.", slugify(db), ".", slugify(plotname)))
                         save_plot(p, outprefix, plotargs$devpars, formats = "png")
+                        if (!is.null(descr)) {
+                            plots[[length(plots) + 1]] <- list(kind = "descr", content = glue::glue(descr))
+                        }
                         plots[[length(plots) + 1]] <- reporter$image(outprefix, c(), FALSE)
                     }
                     reporter$add2(

biopipen/scripts/scrna/ModuleScoreCalculator.R

@@ -1,11 +1,13 @@
-library(Seurat)
+library(rlang)
 library(dplyr)
+library(Seurat)
 library(biopipen.utils)
 
 sobjfile <- {{in.srtobj | r}}
 outfile <- {{out.rdsfile | r}}
 defaults <- {{envs.defaults | r}}
 modules <- {{envs.modules | r}}
+post_mutaters <- {{envs.post_mutaters | r}}
 
 log <- get_logger()
 
@@ -134,6 +136,12 @@ for (key in names(modules)) {
     }
 }
 
+if (!is.null(post_mutaters) && length(post_mutaters) > 0) {
+    log$info("Applying post mutaters ...")
+    sobj@meta.data <- sobj@meta.data %>%
+        mutate(!!!lapply(post_mutaters, parse_expr))
+}
+
 # save seurat object
 log$info("Saving Seurat object ...")
 save_obj(sobj, outfile)

{biopipen-0.34.8.dist-info → biopipen-0.34.10.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: biopipen
-Version: 0.34.8
+Version: 0.34.10
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang
@@ -13,6 +13,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Provides-Extra: runinfo
 Requires-Dist: datar[pandas] (>=0.15.8,<0.16.0)
 Requires-Dist: pipen-board[report] (>=0.17,<0.18)

{biopipen-0.34.8.dist-info → biopipen-0.34.10.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biopipen/__init__.py,sha256=R2kKZIbRrNhrmdllokG5_J0gtqktdwFV00CiImolksE,23
+biopipen/__init__.py,sha256=u7r_X5RPL4hal_HhVAZpDtDz0JbAd6bKAwNi0BAOm5c,24
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
 biopipen/core/config.toml,sha256=lZV_vbYWk6uqm19ZWJcsZCcSNqAdIfN2fOfamzxZpg4,2148
@@ -20,9 +20,9 @@ biopipen/ns/gsea.py,sha256=eMGj6lljdMds2Pzs3Mcab0lQPU4vtgRTKMhAsKXpxYo,9742
 biopipen/ns/misc.py,sha256=0jDPvpRL3EUIf2ipTjKqLTZgnallLWEjSxzTpS-geTQ,4355
 biopipen/ns/plot.py,sha256=N41_izb6zi-XArUly5WhLebapNXbTNSgGlOCCwtrDlY,18282
 biopipen/ns/protein.py,sha256=YJtlKoHI2p5yHdxKeQnNtm5QrbxDGOq1UXOdt_7tlTs,6391
-biopipen/ns/regulatory.py,sha256=gJjGVpJrdv-rg2t5UjK4AGuvtLNymaNYNvoD8PhlbvE,15929
+biopipen/ns/regulatory.py,sha256=WlnX_R8jEFyxCjk8mru5Qu5iCQJLzjMWiWGoc3gygzc,16221
 biopipen/ns/rnaseq.py,sha256=bKAa6friFWof4yDTWZQahm1MS-lrdetO1GqDKdfxXYc,7708
-biopipen/ns/scrna.py,sha256=4dqgsj1cQGFWsJbrbdVF6ElaELmLBg76RlqqGmsW1iA,145087
+biopipen/ns/scrna.py,sha256=ts8yust_YJBb-95Wl59KbEfStML3Eb4fmZInpfatXGc,146298
 biopipen/ns/scrna_metabolic_landscape.py,sha256=EwLMrsj_pTqvyAgtHLoishjQxCg_j8n5OofuTofUph0,22096
 biopipen/ns/snp.py,sha256=iXWrw7Lmhf4_ct57HGT7JGTClCXUD4sZ2FzOgsC2pTg,28123
 biopipen/ns/stats.py,sha256=DlPyK5Vsg6ZEkV9SDS3aAw21eXzvOHgqeZDkXPhg7go,20509
@@ -128,22 +128,22 @@ biopipen/scripts/protein/PDB2Fasta.py,sha256=HVsoRRpieobuPwemCz30_N0rJ7T4aGFTQKZ
 biopipen/scripts/protein/Prodigy.py,sha256=elA62U7WJ89TGEKobvjjd3Refjzr61S69PiVO0qF6DE,4493
 biopipen/scripts/protein/ProdigySummary.R,sha256=qP30GYFpmxCvcfT2IVbJImGMgOdreKi-m1nyUqH6480,3799
 biopipen/scripts/protein/RMSD.py,sha256=zE0g9QKWqqpC8lhGoQIF54VqDw37FaOUkvk0vtYf4-c,6250
-biopipen/scripts/regulatory/MotifAffinityTest.R,sha256=1CUy9domUc3N8FM12bJJYxPSLPwXwwSeHDy7zWf6yAQ,2974
-biopipen/scripts/regulatory/MotifAffinityTest_AtSNP.R,sha256=ZTFrD3g6dDHCb7dZPt7DfkSMFyfMdB8or6clCudMPmw,4366
-biopipen/scripts/regulatory/MotifAffinityTest_MotifBreakR.R,sha256=wx0KM_96iQKmoZ7ZQ8ahSLrOzkyQtsAO41vH3NGxABM,3304
+biopipen/scripts/regulatory/MotifAffinityTest.R,sha256=7kQFV9ExawMkCfLJ-mIsnxbXazL57D1-hVBWcHEPrus,3466
+biopipen/scripts/regulatory/MotifAffinityTest_AtSNP.R,sha256=pFO6SVo_h1lRdNhq-GOX5jD8jF9PlXz0_XnRDpy9RXg,4670
+biopipen/scripts/regulatory/MotifAffinityTest_MotifBreakR.R,sha256=Z-OcUuLPScX5kZvozNGhtawdkbF33ckiuBsSrXRAApk,3853
 biopipen/scripts/regulatory/MotifScan.py,sha256=mxhRWp6NBGEMpWJOpwqIvzkKlrgnRvJApyCU91svh8E,5399
-biopipen/scripts/regulatory/VariantMotifPlot.R,sha256=-uG0gqJsCX1WKohC5-q93cp3Iysl1SzI1PLiKpROl4g,2839
-biopipen/scripts/regulatory/motifs-common.R,sha256=41CqfXtxbbKsk7bF_pG5wq2sNfSR4NzSA5yK2ZG1JtQ,13305
+biopipen/scripts/regulatory/VariantMotifPlot.R,sha256=cHngquU7zVCUhh8zGi40k1o7oeWLfuF78Ycljo_Ql88,2849
+biopipen/scripts/regulatory/motifs-common.R,sha256=ES2UaFE68yULd4mfw7-T0zUcXQtb_uI6IDS-hQsVSvQ,13369
 biopipen/scripts/rnaseq/Simulation-ESCO.R,sha256=cdADB5dpkI5hvzDPw5PyrhOyRFU4PMLgSsa84YOZALc,6424
 biopipen/scripts/rnaseq/Simulation-RUVcorr.R,sha256=oZJHHEMdH7SBIkhCrgkpNYroBkF0dtr20U3ugY9I9hM,1202
 biopipen/scripts/rnaseq/Simulation.R,sha256=LvIjL_onCA8GJR5TPiREUkN_NlMz_ngcw6PezWKc2x0,809
 biopipen/scripts/rnaseq/UnitConversion.R,sha256=xuoj9AdFiCKNztpCmzwCz9VxmUAE-FslZ_LgjOm7dhM,11360
 biopipen/scripts/scrna/AnnData2Seurat.R,sha256=wc5PDbK9TkuJtoXXxF4W1ODylWhyfKWd3vV_AdOcTjM,1118
 biopipen/scripts/scrna/CCPlotR-patch.R,sha256=KpB8fwacBaWaUNjIidcLUkMShLjS4Gq9UY8LUgIITB0,8369
-biopipen/scripts/scrna/CellCellCommunication.py,sha256=Wg0uFSo0Yt0wq6UT1TBodyK8GtWQXGv7hXRfM665paU,4354
-biopipen/scripts/scrna/CellCellCommunicationPlots.R,sha256=4l2EJVd1y94Nfry8fuRL9OSF6AhS8PGBekimpRUu3s8,1919
+biopipen/scripts/scrna/CellCellCommunication.py,sha256=LnEuV8YHOJSYM7Tb_jwLbTQdMSpJw5ChRIiLktcJzSQ,4471
+biopipen/scripts/scrna/CellCellCommunicationPlots.R,sha256=IcqqhVWasSE54PDWaw85u5_yup_YHVNNwZI7oOy9250,2456
 biopipen/scripts/scrna/CellTypeAnnotation-celltypist.R,sha256=CwYR8WWQMf8r7V2CTalG4kxdKnYMtyhpJBe9zP2sQWA,6964
-biopipen/scripts/scrna/CellTypeAnnotation-direct.R,sha256=w3CKRUA9NZfC3TFbU8I35L4XJ6MtVaWX-VnV7ScZlBI,2196
+biopipen/scripts/scrna/CellTypeAnnotation-direct.R,sha256=jwjSBql66ku11b4O_7bIs9zuwbqHiGgrAFDk1tSbwg4,3111
 biopipen/scripts/scrna/CellTypeAnnotation-hitype.R,sha256=vvjhxin4aoA9heecey0dpr6ofirybygY3ApjgtQW89Y,2094
 biopipen/scripts/scrna/CellTypeAnnotation-sccatch.R,sha256=xxB4K1MzBSNQnDxa44s5ExeU67MbncOBf8lGFr7RvwQ,1870
 biopipen/scripts/scrna/CellTypeAnnotation-sctype.R,sha256=1BZ8tOJsB7lRtrYXtImxly-he4gfDTfGqbwK35yJjYw,4604
@@ -155,9 +155,9 @@ biopipen/scripts/scrna/ExprImputation-rmagic.R,sha256=ePgbMZ_3bKbeUrjsMdkdtBM_MS
 biopipen/scripts/scrna/ExprImputation-scimpute.R,sha256=MI_bYfvCDKJsuGntUxfx_-NdrssBoQgL95-DGwJVE5s,1191
 biopipen/scripts/scrna/ExprImputation.R,sha256=GcdZJpkDpq88hRQjtLZY5-byp8V43stEFm5T-pQbU6A,319
 biopipen/scripts/scrna/LoomTo10X.R,sha256=c6F0p1udsL5UOlb84-53K5BsjSDWkdFyYTt5NQmlIec,1059
-biopipen/scripts/scrna/MarkersFinder.R,sha256=-W0rwS4IlR6DsY9gzGBgBN3aYD_7Tyseg2e8mxM6xA0,24796
+biopipen/scripts/scrna/MarkersFinder.R,sha256=qBVdxO8cKTJMtGyJLl2QGRrtdiXOJSLXu6rpZUPkDZk,25437
 biopipen/scripts/scrna/MetaMarkers.R,sha256=BgYaWYEj6obwqaZaDWqNPtxb1IEEAnXAeBE0Ji9PvBA,12426
-biopipen/scripts/scrna/ModuleScoreCalculator.R,sha256=-tByCPk7i070LynAb0z2ANeRxr1QqiKP0dfrJm52jH4,4198
+biopipen/scripts/scrna/ModuleScoreCalculator.R,sha256=_mvo35a-wk5miUb_kMIVwvKK0b6InRa1NKtN8zznGwk,4457
 biopipen/scripts/scrna/PseudoBulkDEG.R,sha256=IuM4hl-KHZ5aaaTqZeylw4b1ZenMZaY4qobD5qxAlHs,25199
 biopipen/scripts/scrna/RadarPlots.R,sha256=Kn1E-hpczuujpgNjR8MqeIIVN-S3PbpmfcKWGKcNCVY,14546
 biopipen/scripts/scrna/SCImpute.R,sha256=dSJOHhmJ3x_72LBRXT72dbCti5oiB85CJ-OjWtqONbk,2958
@@ -284,7 +284,7 @@ biopipen/utils/misc.py,sha256=pDZ-INWVNqHuXYvcjmu8KqNAigkh2lsHy0BxX44CPvc,4048
 biopipen/utils/reference.py,sha256=Oc6IlA1giLxymAuI7DO-IQLHQ7-DbsWzOQE86oTDfMU,5955
 biopipen/utils/reporter.py,sha256=VwLl6xyVDWnGY7NEXyqBlkW8expKJoNQ5iTyZSELf5c,4922
 biopipen/utils/vcf.py,sha256=MmMbAtLUcKPp02jUdk9TzuET2gWSeoWn7xgoOXFysK0,9393
-biopipen-0.34.8.dist-info/METADATA,sha256=uEU4Tv61Ui1QMIK5aUfQJIu4beg4mYyWwhfZ2IQ9M04,975
-biopipen-0.34.8.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-biopipen-0.34.8.dist-info/entry_points.txt,sha256=BYqHGBQJxyFDNLYqgH64ycI5PYwnlqwYcCFsMvJgzAU,653
-biopipen-0.34.8.dist-info/RECORD,,
+biopipen-0.34.10.dist-info/METADATA,sha256=IeN3Cn85Wko4l4ANyDPAxcKF1P5eJQ1SRyBxTfPg6b8,1027
+biopipen-0.34.10.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+biopipen-0.34.10.dist-info/entry_points.txt,sha256=BYqHGBQJxyFDNLYqgH64ycI5PYwnlqwYcCFsMvJgzAU,653
+biopipen-0.34.10.dist-info/RECORD,,

{biopipen-0.34.8.dist-info → biopipen-0.34.10.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.1.3
+Generator: poetry-core 2.2.1
 Root-Is-Purelib: true
 Tag: py3-none-any