biopipen 0.26.0__py3-none-any.whl → 0.26.1__py3-none-any.whl

biopipen/__init__.py

@@ -1 +1 @@
-__version__ = "0.26.0"
+__version__ = "0.26.1"

biopipen/ns/scrna.py

@@ -483,14 +483,18 @@ class SeuratClusterStats(Proc):
             The parameters from the cases can overwrite the default parameters.
             - frac (flag): Whether to output the fraction of cells instead of number.
             - pie (flag): Also output a pie chart?
+            - circos (flag): Also output a circos plot?
             - table (flag): Whether to output a table (in tab-delimited format) and in the report.
             - frac_ofall(flag): Whether to output the fraction against all cells,
                 instead of the fraction in each group.
+                Does not work for circos plot.
                 Only works when `frac` is `True` and `group-by` is specified.
             - transpose (flag): Whether to transpose the cluster and group, that is,
                 using group as the x-axis and cluster to fill the plot.
+                For circos plot, when transposed, the arrows will be drawn from the idents (by `ident`) to the
+                the groups (by `group-by`).
                 Only works when `group-by` is specified.
-            - position (choice): The position of the bars.
+            - position (choice): The position of the bars. Does not work for pie and circos plots.
                 - stack: Use `position_stack()`.
                 - fill: Use `position_fill()`.
                 - dodge: Use `position_dodge()`.
@@ -499,8 +503,13 @@ class SeuratClusterStats(Proc):
             - group-by: The column name in metadata to group the cells.
                 Does NOT support for pie charts.
             - split-by: The column name in metadata to split the cells into different plots.
+                Does NOT support for circos plots.
             - subset: An expression to subset the cells, will be passed to
                 `dplyr::filter()` on metadata.
+            - circos_devpars (ns): The device parameters for the circos plots.
+                - res (type=int): The resolution of the plots.
+                - height (type=int): The height of the plots.
+                - width (type=int): The width of the plots.
             - pie_devpars (ns): The device parameters for the pie charts.
                 - res (type=int): The resolution of the plots.
                 - height (type=int): The height of the plots.
@@ -634,6 +643,7 @@ class SeuratClusterStats(Proc):
         "stats_defaults": {
             "frac": False,
             "pie": False,
+            "circos": False,
             "table": False,
             "position": "auto",
             "frac_ofall": False,
@@ -644,6 +654,7 @@ class SeuratClusterStats(Proc):
             "subset": None,
             "devpars": {"res": 100, "height": 600, "width": 800},
             "pie_devpars": {"res": 100, "height": 600, "width": 800},
+            "circos_devpars": {"res": 100, "height": 600, "width": 600},
         },
         "stats": {
             "Number of cells in each cluster": {
@@ -1142,6 +1153,7 @@ class TopExpressingGenes(Proc):
             markers See below for all libraries.
             <https://maayanlab.cloud/Enrichr/#libraries>
         n (type=int): The number of top expressing genes to find.
+        subset: An expression to subset the cells for each case.
         cases (type=json): If you have multiple cases, you can specify them
             here. The keys are the names of the cases and the values are the
             above options except `mutaters`. If some options are
@@ -1162,6 +1174,7 @@ class TopExpressingGenes(Proc):
         "section": "DEFAULT",
         "dbs": ["KEGG_2021_Human", "MSigDB_Hallmark_2020"],
         "n": 250,
+        "subset": None,
         "cases": {},
     }
     plugin_opts = {

biopipen/scripts/scrna/CellsDistribution.R

@@ -372,6 +372,7 @@ do_case <- function(name, case) {
         # heatmaps
         log_debug("  Preparing pie charts ...")
         hmd <- m %>%
+            arrange(!!sym(case$group_by), !!sym(cby)) %>%
             mutate(!!sym(cby) := paste0("[", !!sym(case$group_by), "] ", !!sym(cby))) %>%
             select(!!sym(cby), CloneGroupClusterSize, seurat_clusters) %>%
             distinct(!!sym(cby), seurat_clusters, .keep_all = TRUE) %>%
@@ -426,6 +427,9 @@ do_case <- function(name, case) {
     if (length(cells_by) == 1) {
         hmsplits <- NULL
         extra_width <- extra_width - 15
+    } else {
+        # keep the row order
+        hmrowlbls <- factor(hmrowlbls, levels = unique(hmrowlbls))
     }
 
     col_fun <- colorRamp2(c(0, max(hmdata, na.rm = T)), c("lightyellow", "purple"))

biopipen/scripts/scrna/SeuratClusterStats-stats.R

@@ -1,4 +1,5 @@
 # Loaded variables: srtfile, outdir, srtobj
+library(circlize)
 
 stats_defaults = {{envs.stats_defaults | r: todot="-"}}
 stats = {{envs.stats | r: todot="-", skip=1}}
@@ -12,6 +13,7 @@ do_one_stats = function(name) {
     case = list_update(stats_defaults, stats[[name]])
     case$devpars = list_update(stats_defaults$devpars, case$devpars)
     case$pie_devpars = list_update(stats_defaults$pie_devpars, case$pie_devpars)
+    case$circos_devpars = list_update(stats_defaults$circos_devpars, case$circos_devpars)
     if (isTRUE(case$pie) && !is.null(case$group.by)) {
         stop(paste0(name, ": pie charts are not supported for group-by"))
     }
@@ -27,6 +29,7 @@ do_one_stats = function(name) {
 
     figfile = file.path(odir, paste0(slugify(name), ".bar.png"))
     piefile = file.path(odir, paste0(slugify(name), ".pie.png"))
+    circosfile = file.path(odir, paste0(slugify(name), ".circos.png"))
     samtablefile = file.path(odir, paste0(slugify(name), ".bysample.txt"))
     tablefile = file.path(odir, paste0(slugify(name), ".txt"))
 
@@ -172,6 +175,40 @@ do_one_stats = function(name) {
             ui = "tabs"
         )
     }
+
+    if (isTRUE(case$circos)) {
+        if (isTRUE(case$transpose)) {
+            circos_df <- plot_df %>%
+                select(from=!!sym(case$ident), to=!!sym(case$group.by), value=.n)
+        } else {
+            circos_df <- plot_df %>%
+                select(from=!!sym(case$group.by), to=!!sym(case$ident), value=.n)
+        }
+
+        png(
+            circosfile,
+            width=case$circos_devpars$width,
+            height=case$circos_devpars$height,
+            res=case$circos_devpars$res
+        )
+        circos.clear()
+        chordDiagram(
+            circos_df,
+            direction = 1,
+            direction.type = c("diffHeight", "arrows"),
+            link.arr.type = "big.arrow"
+        )
+        dev.off()
+
+        add_report(
+            list(
+                name = "Circos plot",
+                contents = list(list(kind = "image", src = circosfile))
+            ),
+            h1 = name,
+            ui = "tabs"
+        )
+    }
 }
 
 sapply(names(stats), do_one_stats)

biopipen/scripts/scrna/TopExpressingGenes.R

@@ -20,6 +20,7 @@ prefix_each <- {{ envs.prefix_each | r }}
 section <- {{ envs.section | r }}
 dbs <- {{ envs.dbs | r }}
 n <- {{ envs.n | r }}
+sset <- {{ envs.subset | r }}
 cases <- {{ envs.cases | r: todot = "-" }}  # nolint
 
 set.seed(8525)
@@ -43,7 +44,8 @@ if (is.null(cases) || length(cases) == 0) {
             prefix_each = prefix_each,
             section = section,
             dbs = dbs,
-            n = n
+            n = n,
+            subset = sset
         )
     )
 } else {
@@ -56,7 +58,8 @@ if (is.null(cases) || length(cases) == 0) {
             prefix_each = prefix_each,
             section = section,
             dbs = dbs,
-            n = n
+            n = n,
+            subset = sset
         )
     })
 }
@@ -144,7 +147,7 @@ casename_info <- function(casename, create = FALSE) {
 }
 
 do_enrich <- function(expr, odir) {
-    log_info("  Saving expressions ...")
+    log_debug("  Saving expressions ...")
     expr <- expr %>% as.data.frame()
     colnames(expr) <- c("Expression")
     expr <- expr %>% rownames_to_column("Gene") %>% select(Gene, Expression)
@@ -165,7 +168,7 @@ do_enrich <- function(expr, odir) {
         quote = FALSE
     )
 
-    log_info("  Running enrichment ...")
+    log_debug("  Running enrichment ...")
     enriched <- enrichr(head(expr$Gene, n), dbs)  # nolint
     for (db in dbs) {
         write.table(
@@ -178,7 +181,7 @@ do_enrich <- function(expr, odir) {
         )
 
         if (nrow(enriched[[db]]) == 0) {
-            log_info(paste0("  No enriched terms for ", db))
+            log_warn(paste0("  No enriched terms for ", db))
             next
         }
 
@@ -199,15 +202,24 @@ do_case <- function(casename) {
     case <- cases[[casename]]
     info <- casename_info(casename, create = TRUE)
 
-    log_info("  Calculating average expression ...")
-    assay <- DefaultAssay(srtobj)
+    log_debug("  Calculating average expression ...")
+    if (!is.null(case$subset)) {
+        tryCatch({
+            sobj <- subset(srtobj, !!parse_expr(case$subset))
+        }, error = function(e) {
+            log_warn("  No cells found for the subset, skipping ...")
+        })
+    } else {
+        sobj <- srtobj
+    }
+    assay <- DefaultAssay(sobj)
     avgexpr <- AverageExpression(
-        srtobj,
+        sobj,
         group.by = case$group.by,
         assays = assay
     )[[assay]]
     # https://github.com/satijalab/seurat/issues/7893
-    colnames(avgexpr) <- as.character(unique(srtobj@meta.data[[case$group.by]]))
+    colnames(avgexpr) <- as.character(unique(sobj@meta.data[[case$group.by]]))
     avgexpr <- avgexpr[, case$ident, drop = FALSE]
     avgexpr <- avgexpr[order(-avgexpr), , drop = FALSE]
 
@@ -217,7 +229,7 @@ do_case <- function(casename) {
 }
 
 add_case_report <- function(info) {
-    log_info("  Adding case report ...")
+    log_debug("  Adding case report ...")
     h1 = ifelse(
         info$section == "DEFAULT",
         info$case,
@@ -237,30 +249,43 @@ add_case_report <- function(info) {
         ifelse(single_section, "#", info$case)
     )
 
-    add_report(
-        list(
-            kind = "descr",
-            content = paste0("Top ", n, " expressing genes")
-        ),
-        list(
-            kind = "table",
-            src = file.path(info$casedir, "exprn.txt")
-        ),
-        h1 = h1,
-        h2 = ifelse(h2 == "#", "Top Expressing Genes", h2),
-        h3 = ifelse(h2 == "#", "#", "Top Expressing Genes")
-    )
+    if (!is.null(info$error)) {
+        add_report(
+            list(
+                kind = "descr",
+                content = paste0("Top ", n, " expressing genes")
+            ),
+            list(kind = "error", content = info$error),
+            h1 = h1,
+            h2 = ifelse(h2 == "#", "Top Expressing Genes", h2),
+            h3 = ifelse(h2 == "#", "#", "Top Expressing Genes")
+        )
+    } else {
+        add_report(
+            list(
+                kind = "descr",
+                content = paste0("Top ", n, " expressing genes")
+            ),
+            list(
+                kind = "table",
+                src = file.path(info$casedir, "exprn.txt")
+            ),
+            h1 = h1,
+            h2 = ifelse(h2 == "#", "Top Expressing Genes", h2),
+            h3 = ifelse(h2 == "#", "#", "Top Expressing Genes")
+        )
 
-    add_report(
-        list(
-            kind = "descr",
-            content = paste0("Enrichment analysis for the top ", n, " expressing genes")
-        ),
-        list(kind = "enrichr", dir = info$casedir),
-        h1 = h1,
-        h2 = ifelse(h2 == "#", "Enrichment Analysis", h2),
-        h3 = ifelse(h2 == "#", "#", "Enrichment Analysis")
-    )
+        add_report(
+            list(
+                kind = "descr",
+                content = paste0("Enrichment analysis for the top ", n, " expressing genes")
+            ),
+            list(kind = "enrichr", dir = info$casedir),
+            h1 = h1,
+            h2 = ifelse(h2 == "#", "Enrichment Analysis", h2),
+            h3 = ifelse(h2 == "#", "#", "Enrichment Analysis")
+        )
+    }
 }
 
 sapply(sort(names(cases)), do_case)

biopipen/scripts/tcr/CloneResidency.R

@@ -329,6 +329,7 @@ plot_venndg <- function(counts, groups, singletons) {
 
 plot_upset <- function(counts, singletons) {
     query_singleton <- function(row) { row["Singletons"] == "true" }
+    query_multiplet <- function(row) { rep(TRUE, length(row)) }
 
     cnts <- column_to_rownames(counts, "CDR3.aa") %>%
         mutate(across(everything(), ~ as.integer(as.logical(.x))))
@@ -342,6 +343,14 @@ plot_upset <- function(counts, singletons) {
     sets <- make.names(sets)
 
     upset(cnts, sets = sets, query.legend = "top", sets.x.label = "# clones", queries = list(
+        list(
+            # in order to add legend
+            # actually mark all, but singleton will override
+            query = query_multiplet,
+            color = "#3b3b3b",
+            active = TRUE,
+            query.name = "Multiplets"
+        ),
         list(
             query = query_singleton,
             color = "orange",

biopipen/utils/misc.R

@@ -29,6 +29,25 @@ bQuote <- function(x) {
 #' @param tolower Convert to lowercase
 #' @return A slugified string
 slugify <- function(x, non_alphanum_replace="-", collapse_replace=TRUE, tolower=FALSE) {
+    subs <- list(
+        "š"="s", "œ"="oe", "ž"="z", "ß"="ss", "þ"="y", "à"="a", "á"="a", "â"="a",
+        "ã"="a", "ä"="a", "å"="a", "æ"="ae", "ç"="c", "è"="e", "é"="e", "ê"="e",
+        "ë"="e", "ì"="i", "í"="i", "î"="i", "ï"="i", "ð"="d", "ñ"="n", "ò"="o",
+        "ó"="o", "ô"="o", "õ"="o", "ö"="o", "ø"="oe", "ù"="u", "ú"="u", "û"="u",
+        "ü"="u", "ý"="y", "ÿ"="y", "ğ"="g", "ı"="i", "ij"="ij", "ľ"="l", "ň"="n",
+        "ř"="r", "ş"="s", "ť"="t", "ų"="u", "ů"="u", "ý"="y", "ź"="z", "ż"="z",
+        "ſ"="s", "α"="a", "β"="b", "γ"="g", "δ"="d", "ε"="e", "ζ"="z", "η"="h",
+        "θ"="th", "ι"="i", "κ"="k", "λ"="l", "μ"="m", "ν"="n", "ξ"="x", "ο"="o",
+        "π"="p", "ρ"="r", "σ"="s", "τ"="t", "υ"="u", "φ"="ph", "χ"="ch", "ψ"="ps",
+        "ω"="o", "ά"="a", "έ"="e", "ή"="h", "ί"="i", "ό"="o", "ύ"="u", "ώ"="o",
+        "ϐ"="b", "ϑ"="th", "ϒ"="y", "ϕ"="ph", "ϖ"="p", "Ϛ"="st", "ϛ"="st", "Ϝ"="f",
+        "ϝ"="f", "Ϟ"="k", "ϟ"="k", "Ϡ"="k", "ϡ"="k", "ϰ"="k", "ϱ"="r", "ϲ"="s",
+        "ϳ"="j", "ϴ"="th", "ϵ"="e", "϶"="p"
+    )
+    # replace latin and greek characters to the closest english character
+    for (k in names(subs)) {
+        x <- gsub(k, subs[[k]], x)
+    }
     x <- gsub("[^[:alnum:]_]", non_alphanum_replace, x)
     if(collapse_replace) x <- gsub(paste0(non_alphanum_replace, "+"), non_alphanum_replace, x)
     if(tolower) x <- tolower(x)

{biopipen-0.26.0.dist-info → biopipen-0.26.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.26.0
+Version: 0.26.1
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

{biopipen-0.26.0.dist-info → biopipen-0.26.1.dist-info}/RECORD

@@ -1,4 +1,4 @@
-biopipen/__init__.py,sha256=S1dNBNSmHJkAHkq1vL1Yg-dFpQk0fri_CstNlL1u5qw,23
+biopipen/__init__.py,sha256=u0eTmljUU0kO8AAW-e1ESQ49mK2SuhpCy7eCliBLlDU,23
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
 biopipen/core/config.toml,sha256=20RCI30Peee1EQdfb_UbV3Hf74XUPndJnYZlUThytsw,1781
@@ -21,7 +21,7 @@ biopipen/ns/gsea.py,sha256=EsNRAPYsagaV2KYgr4Jv0KCnZGqayM209v4yOGGTIOI,7423
 biopipen/ns/misc.py,sha256=fzn0pXvdghMkQhu-e3MMapPNMyO6IAJbtTzVU3GbFa0,3246
 biopipen/ns/plot.py,sha256=yguxmErUOH-hOM10JfuI_sXw2p49XF8yGR_gXfbd5yQ,4066
 biopipen/ns/rnaseq.py,sha256=bKAa6friFWof4yDTWZQahm1MS-lrdetO1GqDKdfxXYc,7708
-biopipen/ns/scrna.py,sha256=ejYfpgB6kB8V7iGPllN7bBJpl44eGp6xuofjT9GxQdI,99051
+biopipen/ns/scrna.py,sha256=Tm4FMMBfHnK99hcrCjIvigYtiIxOSXEemgNmi3qwE8M,99855
 biopipen/ns/scrna_metabolic_landscape.py,sha256=9s1NvH3aMaNDXyfwy9TdzGcSP_lIW4JqhLgknNZcIKE,28313
 biopipen/ns/snp.py,sha256=upGltsjjl09PWcRVdW6D5WpAQ3oWm1KwxQ026wsQwWc,2583
 biopipen/ns/stats.py,sha256=yJ6C1CXF84T7DDs9mgufqUOr89Rl6kybE5ji8Vnx6cw,13693
@@ -123,7 +123,7 @@ biopipen/scripts/scrna/CellTypeAnnotation-hitype.R,sha256=6_DBAlLKcHqaMyWGZWvTd4
 biopipen/scripts/scrna/CellTypeAnnotation-sccatch.R,sha256=1ejye0hs-EOwzzdP9gFWSLPcF6dOAA6VmNKXEjmS11E,1654
 biopipen/scripts/scrna/CellTypeAnnotation-sctype.R,sha256=1nKRtzhVoJ9y0yMg1sgI6u7czsrk2cN0FvNUCZo8l-o,3878
 biopipen/scripts/scrna/CellTypeAnnotation.R,sha256=OwLM_G4D7TG4HhIJjQxgIQM92X86lsWp9MVyXTTkLSc,618
-biopipen/scripts/scrna/CellsDistribution.R,sha256=jeR57kNdh6ibY42x5tO17qkEIFvcn3NQvPywaE-Vob0,19785
+biopipen/scripts/scrna/CellsDistribution.R,sha256=CXdL7yLaoKdkKdgckR6IbUXlVIQQ25oc3CTCq673CEU,19952
 biopipen/scripts/scrna/DimPlots.R,sha256=-mXOTMnpPxvR30XLjwcohFfFx7xTqWKKiICwJiD6yEo,1554
 biopipen/scripts/scrna/ExprImpution-alra.R,sha256=w3W1txJcdWg52-SETY2Z0lO7maDNfiMjBYIGN587YW0,843
 biopipen/scripts/scrna/ExprImpution-rmagic.R,sha256=jYIfqZpnvjKJkvItLnemPVtUApHBYQi1_L8rHVbEe1M,735
@@ -140,7 +140,7 @@ biopipen/scripts/scrna/SeuratClusterStats-dimplots.R,sha256=pZKv1SnSNEGXDeE0_2VY
 biopipen/scripts/scrna/SeuratClusterStats-features.R,sha256=SaKTJloP1fttRXZQeb2ApX0ej7al13wOoEYkthSk13k,15489
 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=CE9989SaO75_KYEEVqivEbUoTcUOtiTkRGWLNtWzxI8,6450
+biopipen/scripts/scrna/SeuratClusterStats-stats.R,sha256=b5oXWb2GKt8nQxEXTc8Duv8rSx4UEwaO4OaEdyCBiF0,7590
 biopipen/scripts/scrna/SeuratClusterStats.R,sha256=ouWoj7Q644uG3MUlT23AES8f74g38-jPtPhINSvoUas,1267
 biopipen/scripts/scrna/SeuratClustering.R,sha256=kAvQq3RV86_KSv9NlUtUeQrPKkbhSsnv6Q4DoiTu8M0,6403
 biopipen/scripts/scrna/SeuratFilter.R,sha256=BrYK0MLdaTtQvInMaQsmOt7oH_hlks0M1zykkJtg2lM,509
@@ -152,7 +152,7 @@ biopipen/scripts/scrna/SeuratSplit.R,sha256=vdK11V39_Uo_NaOh76QWCtxObGaEr5Ynxqq0
 biopipen/scripts/scrna/SeuratSubClustering.R,sha256=L1SwKhNNKvsQGrcj0ZjScW9BLuvdO2pg7U48Ospsot8,6096
 biopipen/scripts/scrna/SeuratSubset.R,sha256=yVA11NVE2FSSw-DhxQcJRapns0tNNHdyDYi5epO6SKM,1776
 biopipen/scripts/scrna/SeuratTo10X.R,sha256=T2nJBTwOe12AIKC2FZsMSv6xx3s-67CYZokpz5wshqY,2679
-biopipen/scripts/scrna/TopExpressingGenes.R,sha256=J6tM54HStWkguUwFoIHRo_EAtCUKOuCBEfInzRfDYMQ,7703
+biopipen/scripts/scrna/TopExpressingGenes.R,sha256=1OTCBeHooAKkByDBSBNG5F2icrPuznDW92EgG3YazTw,8563
 biopipen/scripts/scrna/Write10X.R,sha256=OMhXvJwvaH-aWsMpijKrvXQVabc1qUu5ZEwiLAhkDeY,285
 biopipen/scripts/scrna/celltypist-wrapper.py,sha256=f5M8f4rU5nC7l17RS0YVmUPpLLz4D6PIcgWtA77UExM,1722
 biopipen/scripts/scrna/sctype.R,sha256=NaUJkABwF5G1UVm1CCtcMbwLSj94Mo24mbYCKFqo1Bw,6524
@@ -170,7 +170,7 @@ biopipen/scripts/tcgamaf/MafAddChr.py,sha256=V10HMisl12O3ZfXuRmFNdy5p-3mr43WCvy0
 biopipen/scripts/tcgamaf/maf2vcf.pl,sha256=hJKcH-NbgWK6fmK7f3qex7ozJJl-PqCNPXqpwfcHwJg,22707
 biopipen/scripts/tcr/Attach2Seurat.R,sha256=C91TAh1cLSxWkdFPf84pbxlpTYMuWq_rduG4eiIkXZI,1345
 biopipen/scripts/tcr/CDR3AAPhyschem.R,sha256=-0BS6cdt5GfQJphA3HlDgGjWr4XFF-7INLJyMBHQNAc,16628
-biopipen/scripts/tcr/CloneResidency.R,sha256=heL5bV8ZjMtHlUditFDciIavOb7NUpw8vLI6PeP-R40,20027
+biopipen/scripts/tcr/CloneResidency.R,sha256=AVIsBIR1zEuaQ9ozb0dbe9BSYi-RMV2-83xKPZ6DVMU,20347
 biopipen/scripts/tcr/CloneSizeQQPlot.R,sha256=5FPfWQjxTsv59KSDQaDWj3C95zPQMngKG7qOf95NEzI,4527
 biopipen/scripts/tcr/GIANA/GIANA.py,sha256=0qLhgCWxT8K-4JvORA03CzBPTT5pd4Di5B_DgrHXbFA,47198
 biopipen/scripts/tcr/GIANA/GIANA4.py,sha256=Z7Q3cUr1Pvmy4CFADN0P7i9g1-HbzWROMqk5HvL_F1Q,45762
@@ -229,7 +229,7 @@ biopipen/utils/gene.R,sha256=BzAwlLA8hO12vF-3t6IwEuTEeLa_jBll4zm_5qe3qoE,1243
 biopipen/utils/gene.py,sha256=qE_BqTayrJWxRdniffhcz6OhZcw9GUoOrj2EtFWH9Gw,2246
 biopipen/utils/gsea.R,sha256=UMQOlWGstQTOBScvy1wIzrB7I3CE28Xo2v1sy4lmJ-M,7549
 biopipen/utils/io.R,sha256=jIYdqdn0iRWfQYAZa5CjXi3fikqmYvPPLIXhobRe8sw,537
-biopipen/utils/misc.R,sha256=sB2cM-sJn9H90FAZD89uNUYPU5k_6BT8d_nG33fI7d4,5520
+biopipen/utils/misc.R,sha256=yo6mp6lBiKCPpSuAmfETNJSQJDduTbEXa_56jmqs_VE,6805
 biopipen/utils/misc.py,sha256=BpqPVgp_IlsUZow5P4mEtbPMjhO_vEb5atrF7iJ_xhU,3509
 biopipen/utils/mutate_helpers.R,sha256=Bqy6Oi4rrPEPJw0Jq32bVAwwBfZv7JJL9jFcK5x-cek,17649
 biopipen/utils/plot.R,sha256=pzl37PomNeUZPxohHZ2w93j3Fc4T0Qrc62FF-9MTKdw,4417
@@ -237,7 +237,7 @@ biopipen/utils/reference.py,sha256=6bPSwQa-GiDfr7xLR9a5T64Ey40y24yn3QfQ5wDFZkU,4
 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-0.26.0.dist-info/METADATA,sha256=kyC-B-tDvcgEtVjGgqbyobl0IUKgVcYl7Vwa959Arz0,878
-biopipen-0.26.0.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-biopipen-0.26.0.dist-info/entry_points.txt,sha256=mf2ju-IhPRJtq0wHOKJAYIwhrRt41QFOfAOYwMfYyh4,625
-biopipen-0.26.0.dist-info/RECORD,,
+biopipen-0.26.1.dist-info/METADATA,sha256=jpb9Z7AVsQ7LN-Zhza6QDrD1yDPWBuIcOwrajRsJV5M,878
+biopipen-0.26.1.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+biopipen-0.26.1.dist-info/entry_points.txt,sha256=wu70aoBcv1UahVbB_5237MY-9M9_mzqmWjDD-oi3yz0,621
+biopipen-0.26.1.dist-info/RECORD,,

{biopipen-0.26.0.dist-info → biopipen-0.26.1.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.8.1
+Generator: poetry-core 1.9.0
 Root-Is-Purelib: true
 Tag: py3-none-any

{biopipen-0.26.0.dist-info → biopipen-0.26.1.dist-info}/entry_points.txt

@@ -11,11 +11,11 @@ delim=biopipen.ns.delim
 gene=biopipen.ns.gene
 gsea=biopipen.ns.gsea
 misc=biopipen.ns.misc
-plink=biopipen.ns.plink
 plot=biopipen.ns.plot
 rnaseq=biopipen.ns.rnaseq
 scrna=biopipen.ns.scrna
 scrna_metabolic_landscape=biopipen.ns.scrna_metabolic_landscape
+snp=biopipen.ns.snp
 stats=biopipen.ns.stats
 tcgamaf=biopipen.ns.tcgamaf
 tcr=biopipen.ns.tcr