biopipen 0.22.0__py3-none-any.whl → 0.22.2__py3-none-any.whl

biopipen/utils/mutate_helpers.R

@@ -1,6 +1,7 @@
 suppressPackageStartupMessages(library(rlang))
 suppressPackageStartupMessages(library(tidyselect))
 suppressPackageStartupMessages(library(dplyr))
+suppressPackageStartupMessages(library(tidyr))
 
 #' Get expanded, collapsed, emerged or vanished clones from a meta data frame
 #'
@@ -15,6 +16,8 @@ suppressPackageStartupMessages(library(dplyr))
 #'  be used as `ident_2`.
 #' @param subset An expression to subset the cells, will be passed to
 #'  `dplyr::filter()`. Default is `TRUE` (no filtering).
+#' @param each A column name (without quotes) in metadata to split the cells.
+#'  Each comparison will be done for each value in this column.
 #' @param id The column name (without quotes) in metadata for the
 #'  group ids (i.e. `CDR3.aa`)
 #' @param compare Either a (numeric) column name (i.e. `Clones`, without quotes)
@@ -25,6 +28,7 @@ suppressPackageStartupMessages(library(dplyr))
 #' @param uniq Whether to return unique ids or not. Default is `TRUE`.
 #'  If `FALSE`, you can mutate the meta data frame with the returned ids.
 #'  For example, `df %>% mutate(expanded = expanded(...))`.
+#' @param debug Return the transformed data frame with counts, predicates, sum, and diff.
 #' @param order The order of the returned ids. It could be `sum` or `diff`,
 #'  which is the sum or diff of the `compare` between idents. Two kinds of
 #'  modifiers can be added, including `desc` and `abs`. For example,
@@ -82,8 +86,10 @@ suppressPackageStartupMessages(library(dplyr))
     id,
     compare,
     fun,
+    each,
     uniq,
-    order
+    order,
+    debug
 ) {
     if (length(idents) == 1) {
         ident_1 <- idents[1]
@@ -119,100 +125,82 @@ suppressPackageStartupMessages(library(dplyr))
 
     if (!compare_is_count && !compare_label %in% colnames(df)) {
         stop(paste0(
-            "`compare` must be either a column name in df, or 'count'/'n'. ",
+            "`compare` must be either a column name in df, or 'count'/'.n'. ",
             'Got "',
             compare_label,
             '"'
         ))
     }
 
-    predicate <- function(comp) {
+    predicate <- function(ident_1, ident_2) {
         if (fun == "expanded") {
-            comp[1] > comp[2] && comp[2] > 0
+            ident_1 > ident_2 && ident_2 > 0
         } else if (fun == "expanded+") {
-            comp[1] > comp[2]
+            ident_1 > ident_2
         } else if (fun == "collapsed") {
-            comp[1] < comp[2] && comp[1] > 0
+            ident_1 < ident_2 && ident_1 > 0
         } else if (fun == "collapsed+") {
-            comp[1] < comp[2]
+            ident_1 < ident_2
         } else if (fun == "emerged") {
-            comp[1] > 0 && comp[2] == 0
+            ident_1 > 0 && ident_2 == 0
         } else if (fun == "vanished") {
-            comp[1] == 0 && comp[2] > 0
+            ident_1 == 0 && ident_2 > 0
         }
     }
 
     # subset the data frame
-    trans <- df %>% dplyr::filter(!!subset) %>%
-        # remove NA values in group.by column
-        dplyr::filter(!is.na(!!group.by)) %>%
-        # mark the group.by column (as ..group) as ident_1 or ident_2 or NA
+    trans <- df %>%
+        dplyr::filter(!!subset) %>%
+        drop_na(!!id) %>%
+        # # remove NA values in group.by column
+        # dplyr::filter(!is.na(!!group.by)) %>%
+        # mark the group.by column (as .group) as ident_1 or ident_2 or NA
         mutate(
-            ..group = if_else(
+            .group = if_else(
                 !!group.by == ident_1,
                 "ident_1",
                 if_else(ident_2 != "<NULL>" & !!group.by != ident_2, NA, "ident_2")
             )
         ) %>%
         # remove NA values in ..group column
-        dplyr::filter(!is.na(..group)) %>%
-        # for each clone and group (ident_1 and ident_2)
-        group_by(!!id, ..group) %>%
-        # summarise the number of cells in each clone and group
-        # so that we can compare between groups later
-        summarise(
-            ..compare = ifelse(compare_is_count, n(), first(!!compare)),
-            .groups = "drop"
-        ) %>%
-        # for each clone, either compare Clones or ..count between groups
-        # (ident_1 and ident_2)
-        group_by(!!id) %>%
-        # add missing group (either ident_1 or ident_2)
-        group_modify(function(d, ...) {
-            if (nrow(d) == 1) {
-                d <- d %>% add_row(
-                    ..group = ifelse(
-                        d$..group == "ident_1", "ident_2", "ident_1"
-                    ),
-                    ..compare = 0
-                )
-            }
-            d
-        }) %>%
-        # make sure ident_1 and ident_2 are in order
-        arrange(..group, .by_group = TRUE) %>%
+        drop_na(.group)
+
+    if (is.null(each)) {
+        trans <- trans %>% group_by(!!id, .group)
+    } else {
+        trans <- trans %>% group_by(!!each, !!id, .group)
+    }
+
+    if (compare_is_count) {
+        trans <- trans %>% summarise(.n = n(), .groups = "drop")
+    } else {
+        trans <- trans %>% summarise(.n = first(!!compare), .groups = "drop")
+    }
+
+    trans <- trans %>% pivot_wider(names_from = .group, values_from = .n) %>%
+        replace_na(list(ident_1 = 0, ident_2 = 0)) %>%
+        rowwise() %>%
         # add the predicates, sums and diffs
-        summarise(
-            ..predicate = predicate(..compare),
-            ..sum = sum(..compare),
-            ..diff = ..compare[1] - ..compare[2]
+        mutate(
+            .predicate = predicate(ident_1, ident_2),
+            .sum = ident_1 + ident_2,
+            .diff = ident_1 - ident_2
         ) %>%
-        # filter the clones
-        dplyr::filter(..predicate)
+        ungroup() %>%
+        arrange(!!order)
 
-    order_sum <- grepl("sum", order)
-    order_diff <- grepl("diff", order)
-    order_desc <- grepl("desc", order)
-    order_abs <- grepl("abs", order)
-    if (order_sum && !order_desc) {
-        out <- trans %>% arrange(..sum) %>% pull(!!id)
-    } else if (order_sum) {
-        out <- trans %>% arrange(desc(..sum)) %>% pull(!!id)
-    } else if (order_diff && !order_desc && !order_abs) {
-        out <- trans %>% arrange(..diff) %>% pull(!!id)
-    } else if (order_diff && !order_desc && order_abs) {
-        out <- trans %>% arrange(abs(..diff)) %>% pull(!!id)
-    } else if (order_diff && order_desc && !order_abs) {
-        out <- trans %>% arrange(desc(..diff)) %>% pull(!!id)
-    } else if (order_diff && order_desc && order_abs) {
-        out <- trans %>% arrange(desc(abs(..diff))) %>% pull(!!id)
-    } else {
-        out <- trans %>% pull(!!id)
+    if (debug) {
+        return(trans)
     }
 
-    if (uniq) { return(out) }
+    uniq_ids <- trans %>% filter(.predicate) %>% pull(!!id) %>% as.vector() %>% unique()
+    if (uniq) {
+        return(uniq_ids)
+    }
 
-    df %>% mutate(..out = if_else(!!id %in% out, !!id, NA)) %>% pull(..out)
+    out <- df %>% pull(!!id)
+    out[!out %in% uniq_ids] <- NA
+    out
 }
 
 #' @export
@@ -221,10 +209,12 @@ expanded <- function(
     group.by, # nolint
     idents,
     subset = TRUE,
+    each = NULL,
     id = CDR3.aa,
-    compare = Clones,
+    compare = .n,
     uniq = TRUE,
-    order = "diff+desc",
+    debug = FALSE,
+    order = desc(.sum),
     include_emerged = FALSE
 ) {
     lbl <- as_label(enquo(df))
@@ -233,15 +223,17 @@ expanded <- function(
     }
     fun = if (include_emerged) "expanded+" else "expanded"
     .size_compare(
-        df,
-        enquo(group.by),
-        idents,
-        enquo(subset),
-        enquo(id),
-        enquo(compare),
-        fun,
+        df = df,
+        group.by = enquo(group.by),
+        idents = idents,
+        subset = enquo(subset),
+        id = enquo(id),
+        compare = enquo(compare),
+        fun = fun,
+        each = tryCatch(enquo(each), error = function(e) NULL),
         uniq = uniq,
-        order = order
+        order = enexpr(order),
+        debug = debug
     )
 }
 
@@ -251,10 +243,12 @@ collapsed <- function(
     group.by, # nolint
     idents,
     subset = TRUE,
+    each = NULL,
     id = CDR3.aa,
-    compare = Clones,
+    compare = .n,
     uniq = TRUE,
-    order = "diff+desc",
+    debug = FALSE,
+    order = desc(.sum),
     include_vanished = FALSE
 ) {
     lbl <- as_label(enquo(df))
@@ -263,15 +257,17 @@ collapsed <- function(
     }
     fun = if (include_vanished) "collapsed+" else "collapsed"
     .size_compare(
-        df,
-        enquo(group.by),
-        idents,
-        enquo(subset),
-        enquo(id),
-        enquo(compare),
-        fun,
+        df = df,
+        group.by = enquo(group.by),
+        idents = idents,
+        subset = enquo(subset),
+        id = enquo(id),
+        compare = enquo(compare),
+        fun = fun,
+        each = tryCatch(enquo(each), error = function(e) NULL),
         uniq = uniq,
-        order = order
+        order = enexpr(order),
+        debug = debug
     )
 }
 
@@ -281,25 +277,29 @@ emerged <- function(
     group.by, # nolint
     idents,
     subset = TRUE,
+    each = NULL,
     id = CDR3.aa,
-    compare = Clones,
+    compare = .n,
     uniq = TRUE,
-    order = "diff+desc"
+    debug = FALSE,
+    order = desc(.sum)
 ) {
     lbl <- as_label(enquo(df))
     if (length(lbl) == 1 && lbl == ".") {
         df <- across(everything())
     }
     .size_compare(
-        df,
-        enquo(group.by),
-        idents,
-        enquo(subset),
-        enquo(id),
-        enquo(compare),
-        "emerged",
+        df = df,
+        group.by = enquo(group.by),
+        idents = idents,
+        subset = enquo(subset),
+        id = enquo(id),
+        compare = enquo(compare),
+        fun = "emerged",
+        each = tryCatch(enquo(each), error = function(e) NULL),
         uniq = uniq,
-        order = order
+        order = enexpr(order),
+        debug = debug
     )
 }
 
@@ -309,25 +309,29 @@ vanished <- function(
     group.by, # nolint
     idents,
     subset = TRUE,
+    each = NULL,
     id = CDR3.aa,
-    compare = Clones,
+    compare = .n,
     uniq = TRUE,
-    order = "diff+desc"
+    debug = FALSE,
+    order = desc(.sum)
 ) {
     lbl <- as_label(enquo(df))
     if (length(lbl) == 1 && lbl == ".") {
         df <- across(everything())
     }
     .size_compare(
-        df,
-        enquo(group.by),
-        idents,
-        enquo(subset),
-        enquo(id),
-        enquo(compare),
-        "vanished",
+        df = df,
+        group.by = enquo(group.by),
+        idents = idents,
+        subset = enquo(subset),
+        id = enquo(id),
+        compare = enquo(compare),
+        fun = "vanished",
+        each = tryCatch(enquo(each), error = function(e) NULL),
         uniq = uniq,
-        order = order
+        order = enexpr(order),
+        debug = debug
     )
 }
 

{biopipen-0.22.0.dist-info → biopipen-0.22.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.22.0
+Version: 0.22.2
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

{biopipen-0.22.0.dist-info → biopipen-0.22.2.dist-info}/RECORD

@@ -1,15 +1,16 @@
-biopipen/__init__.py,sha256=0kk8efeJF41FZIYweGTJylbizaWrp9W3qN78RClCWIU,23
+biopipen/__init__.py,sha256=Bh5Z0gPzleot68P4r2qTs7W0HNi5DFO8t_uKNyCoA94,23
 biopipen/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/core/config.py,sha256=edK5xnDhM8j27srDzsxubi934NMrglLoKrdcC8qsEPk,1069
-biopipen/core/config.toml,sha256=JALO2S7TfmV3gIRPJ0cLTFWncPXXheQJS3vYQlyX6wQ,1600
+biopipen/core/config.toml,sha256=Rn7Cta7WsMtmQkKGC4h9d5dU_STaIVBgR8UliiGgL6o,1757
 biopipen/core/defaults.py,sha256=yPeehPLk_OYCf71IgRVCWuQRxLAMixDF81Ium0HtPKI,344
-biopipen/core/filters.py,sha256=5Qi7do0JT8_mwd80ddf4TgsX7yZh__ZpOex270Jjrbc,11037
+biopipen/core/filters.py,sha256=bsH5an2Wfk4JaEEYpa5xFLy9-QVN3fdA_nl7_ceSM68,11562
 biopipen/core/proc.py,sha256=7TsjBM7EEtMMB-w4jbxV_CSRY8J970gM8320Ga1YeHU,717
 biopipen/core/testing.py,sha256=5vR15kkCjfXM7Bx0HBzabNLtDLAEX4uU94TskCkPni8,1447
 biopipen/ns/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biopipen/ns/bam.py,sha256=5AsYrB0mtr_mH6mCL6gjJ5rC4NywpjFkpFjUrBGp7Fk,9301
 biopipen/ns/bcftools.py,sha256=puCDfIL-1z6cz2y1Rlz-ESNIr8xJgeIjEQ440qicCvM,3467
 biopipen/ns/bed.py,sha256=UN38qUChDeE-ipuSBY8RVLwvJqM2wxSRmlhOiDo4JG0,5395
+biopipen/ns/cellranger.py,sha256=0A6pCpBLg1zKm2Ve2cXvGvNNK4lMqdsek2iTer5X_TI,3679
 biopipen/ns/cnv.py,sha256=vq6dZfEOyuVuqg3nP6FQtNmQ-JocpBJMX9IYlZ0OPD0,6803
 biopipen/ns/cnvkit.py,sha256=5mA2Q8-YDs4g1HoxtpB_NWnyZYwEThNr3s3wlubLQrQ,31130
 biopipen/ns/cnvkit_pipeline.py,sha256=2fJLn70L2jJ81ZMNdnU84Sf3HoKA2CSnHuDzLGR8jmw,36854
@@ -19,16 +20,18 @@ 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=l4vFeRasGhkexopGTM_VfSyIFewOxg-9L5niFzhWUNA,565
-biopipen/ns/scrna.py,sha256=F5j1TmjsS2swwm-uDyT6sTys5pldIJ_M2hNITAQdflc,82728
+biopipen/ns/scrna.py,sha256=jLK_K90B36ZbmDZcR8PT2x1ntBpvxKHzeNhWYkrexhM,82876
 biopipen/ns/scrna_basic.py,sha256=Py90IveDI5Alm6FUeC89xp3W79VPRvAQctQpc5JtO2M,8639
 biopipen/ns/scrna_metabolic_landscape.py,sha256=dSL-y1Gx1fcgebX7vk3wcSbm9aBALfCZKz0vjcDxQ_8,28139
 biopipen/ns/tcgamaf.py,sha256=AFbUJIxiMSvsVY3RcHgjRFuMnNh2DG3Mr5slLNEyz6o,1455
-biopipen/ns/tcr.py,sha256=-cHx2VjfcYUIwWh1OpEfjHDe3RPH-GDlLnpS4pljUs8,82417
+biopipen/ns/tcr.py,sha256=ZCwL_1Of-F5xVJ0hgdVLAjHwwwfegqkW_SO66oYULqM,83738
 biopipen/ns/vcf.py,sha256=cdkKroii0_nl_bSP2cnO09qESUAhHqu6btOiTSKS79Y,15314
 biopipen/ns/web.py,sha256=3zucrDo-IVsSnIvlw-deoScuxqWa6OMTm8Vo-R4E44Q,2224
 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
+biopipen/reports/cellranger/CellRangerCount.svelte,sha256=oR7WzqY_FcjeCi5rir0qyUdUe09mkYBgg4-V1dB9ph4,478
+biopipen/reports/cellranger/CellRangerVdj.svelte,sha256=oR7WzqY_FcjeCi5rir0qyUdUe09mkYBgg4-V1dB9ph4,478
 biopipen/reports/cnv/AneuploidyScore.svelte,sha256=x0LbhqjauZpqMzmzDWmYgx-rEh5Tzo8qBrXcLcM0h78,1020
 biopipen/reports/cnv/AneuploidyScoreSummary.svelte,sha256=AWlns70mChJGhH3z8r5uXuI4tc7VbVN_cOUdqBr3ZKg,4414
 biopipen/reports/cnv/TMADScoreSummary.svelte,sha256=tJutaMOqeXxKroAosOIqOJVyhTTFet-soMwuOYVHTYU,2060
@@ -76,6 +79,8 @@ biopipen/scripts/bed/Bed2Vcf.py,sha256=u0mp_2Y4UtEA839zq9UENesH6Gyiwd4sZQW9wFnBV
 biopipen/scripts/bed/BedConsensus.py,sha256=gfAxuIalvCEpS0tiOyAJGPYGgHN0L-hm0K37Iteh5yw,2386
 biopipen/scripts/bed/BedLiftOver.sh,sha256=Y4gBsz9w4zhE29UmWojO6F4PXMMMWC1uCzjrxa19eOs,256
 biopipen/scripts/bed/BedtoolsMerge.py,sha256=TjKO5MpUzDj931bQAWku2660MVSiZzdMHt_v2Xbt0IE,355
+biopipen/scripts/cellranger/CellRangerCount.py,sha256=ZDcry8suLhulXiTsl01LGKmSJkewJ-TgHazLtfsBr6U,2516
+biopipen/scripts/cellranger/CellRangerVdj.py,sha256=-QbhPKqFBZ15Es6NJaU7Lwf1KQW_3Lyv0aISh-Urk2M,2504
 biopipen/scripts/cnv/AneuploidyScore.R,sha256=liAN8u8_lj8voJ01oBW9Dw09yi388KF5f_gwPOv0wdE,8437
 biopipen/scripts/cnv/AneuploidyScoreSummary.R,sha256=9Zni5zqYfzevs5XSAt3fqD9WZ_RWr_ByUnXReKLLWoY,12337
 biopipen/scripts/cnv/TMADScore.R,sha256=uCLHQR6sMt-4uVUAEJlJxYXlai9ZE5J7xBl0sl-EkjU,1065
@@ -105,33 +110,33 @@ biopipen/scripts/misc/Str2File.py,sha256=99oQNxChxChNJ9vmD77b48cu-r_P_heSpx7A5wi
 biopipen/scripts/plot/Heatmap.R,sha256=4v_oRME8ZiwczIlBIp-OP_YPWLAvBKzbHiwNBCZ0Xog,1982
 biopipen/scripts/plot/VennDiagram.R,sha256=GVc-kyHqnXrbXZvy-evcxI1XGtlLSChBiVnMjPywNMA,731
 biopipen/scripts/rnaseq/UnitConversion.R,sha256=9etSQ6ivtlrgSg4mLjViZAl8nUtCxfEROxXvFCpN9sg,1928
-biopipen/scripts/scrna/CellTypeAnnotation-direct.R,sha256=jBEc2OTjC4hbVCJJXzZ4KC9Db5W-7kfJ3N5U5rE05AQ,1449
+biopipen/scripts/scrna/CellTypeAnnotation-direct.R,sha256=Qp8w3-Xh67F6QHYzpTjWdSDdCVlhcjGjgoAi7PGUbmI,1797
 biopipen/scripts/scrna/CellTypeAnnotation-hitype.R,sha256=6_DBAlLKcHqaMyWGZWvTd4gFfHymfz9s2XLja8aj1qA,1869
 biopipen/scripts/scrna/CellTypeAnnotation-sccatch.R,sha256=1ejye0hs-EOwzzdP9gFWSLPcF6dOAA6VmNKXEjmS11E,1654
 biopipen/scripts/scrna/CellTypeAnnotation-sctype.R,sha256=u1eQsBWv1GKTbkwp6OFyiPuMFFcgwoa4-VI-d4q8nM4,3877
 biopipen/scripts/scrna/CellTypeAnnotation.R,sha256=6Le1SvZcKI8D0SLkFZ5SibGsW9ZWqirnBl3Q1BNZOuU,513
-biopipen/scripts/scrna/CellsDistribution.R,sha256=iuDGlfHNzenACW2y4KGRtwDQAI650XJ4SSMts7UDXS0,12734
+biopipen/scripts/scrna/CellsDistribution.R,sha256=shfgljiveRMrMM9GAbvemn9vSUCL9vNwTxH2Hiq9Yyk,12669
 biopipen/scripts/scrna/DimPlots.R,sha256=-mXOTMnpPxvR30XLjwcohFfFx7xTqWKKiICwJiD6yEo,1554
 biopipen/scripts/scrna/ExprImpution-alra.R,sha256=8wcyZk1Whf45SXsYOM_ykl8m-iBxr27KEjtslbl2JQQ,782
 biopipen/scripts/scrna/ExprImpution-rmagic.R,sha256=yYnkyVfqIaNynsbaZZLGS6DrAJ_XhVQj1Ox598w8yOY,651
 biopipen/scripts/scrna/ExprImpution-scimpute.R,sha256=mg40qCUW7-nP5oHPvARq7dmtoahM0GRFWXQpum0BXVk,1082
 biopipen/scripts/scrna/ExprImpution.R,sha256=7768ezrr59xUZDXq8lO9jj2XhnkSsx-xxBmOD9_DO7c,313
 biopipen/scripts/scrna/GeneExpressionInvistigation.R,sha256=FI5MWic3xRml2DN7ONcyT7pbceOnL30Zd4nBHRZRFNQ,3800
-biopipen/scripts/scrna/MarkersFinder.R,sha256=mPyKZcYcrhTjLqqp406-wkGZzpTUSBUQnDSsGJe-SL4,18669
+biopipen/scripts/scrna/MarkersFinder.R,sha256=v_PIhg-QcuaY_6F_sNGMkNohLmlZL_BkGNiXNPxRn6I,21137
 biopipen/scripts/scrna/MetaMarkers.R,sha256=3gZdMjO4sGQLq0XvlLooMrQUKEAIYUCTsxVHrkYe7HM,11119
 biopipen/scripts/scrna/ModuleScoreCalculator.R,sha256=0mLGoTvJRpTbCnmuYbYKqZnP3ZdJQkTn6getJddBKRs,2495
 biopipen/scripts/scrna/RadarPlots.R,sha256=1oicly0wxLaQDrDUojKtyCD052cYnMrBcW8TpbFY7wE,8535
 biopipen/scripts/scrna/SCImpute.R,sha256=dSJOHhmJ3x_72LBRXT72dbCti5oiB85CJ-OjWtqONbk,2958
 biopipen/scripts/scrna/ScFGSEA.R,sha256=wePSQYGjGv_InJEmi0Hf0zNt1gmqhkItjFqYE-wiYec,5999
 biopipen/scripts/scrna/SeuratClusterStats-dimplots.R,sha256=BknWb-5Vc_LHB3hlOgsAEooHObG6xoU1JV2KeNVrEGk,1623
-biopipen/scripts/scrna/SeuratClusterStats-features.R,sha256=NLdv5un_mntsNSukChUCXY3u41GARrNMqM4Ko0kN384,7705
+biopipen/scripts/scrna/SeuratClusterStats-features.R,sha256=ft1sSF2pXuDb4H2vSkPYuzcDgOOpXpCZGv9_17DdZN8,7705
 biopipen/scripts/scrna/SeuratClusterStats-stats.R,sha256=KSD4GSssj-UZeMlWPbHbCLyonACGhSvVwAD4jeoJ_60,4099
 biopipen/scripts/scrna/SeuratClusterStats.R,sha256=SO4AGgF95YoLvjGMiC6fb3OIQkXne2Lqt5G7n50JYJo,616
 biopipen/scripts/scrna/SeuratClustering.R,sha256=JBJkwZmdjMsWzHaa_WvYCN1tXQimgclmgAOj3VJ1b3A,9114
 biopipen/scripts/scrna/SeuratFilter.R,sha256=BrYK0MLdaTtQvInMaQsmOt7oH_hlks0M1zykkJtg2lM,509
 biopipen/scripts/scrna/SeuratLoading.R,sha256=ekWKnHIqtQb3kHVQiVymAHXXqiUxs6KKefjZKjaykmk,900
 biopipen/scripts/scrna/SeuratMap2Ref.R,sha256=TkDSDc5do6BOtkAq3fS5HpjyqWUwsu8YqRC5in62oz8,3750
-biopipen/scripts/scrna/SeuratMetadataMutater.R,sha256=YvuhTKTWT7Se3hTqkgD3Ag_PKqKXiyDi6HcGCNIIKiM,723
+biopipen/scripts/scrna/SeuratMetadataMutater.R,sha256=Pp4GsF3hZ6ZC2vroC3LSBmVa4B1p2L3hbh981yaAIeQ,1093
 biopipen/scripts/scrna/SeuratPreparing.R,sha256=j_t8EbPoNNRFPquerYd6BjtbIgdHCt8h2XXZax8_tXM,8453
 biopipen/scripts/scrna/SeuratSplit.R,sha256=vdK11V39_Uo_NaOh76QWCtxObGaEr5Ynxqq0hTiSvsU,754
 biopipen/scripts/scrna/SeuratSubset.R,sha256=yVA11NVE2FSSw-DhxQcJRapns0tNNHdyDYi5epO6SKM,1776
@@ -146,8 +151,8 @@ biopipen/scripts/scrna_metabolic_landscape/MetabolicPathwayHeterogeneity.R,sha25
 biopipen/scripts/tcgamaf/Maf2Vcf.py,sha256=Cxh7fiSNCxWDTfIJqZDOOnaSrw-85S_fH2U-PWY03hc,704
 biopipen/scripts/tcgamaf/MafAddChr.py,sha256=V10HMisl12O3ZfXuRmFNdy5p-3mr43WCvy0GHxSpwfA,494
 biopipen/scripts/tcgamaf/maf2vcf.pl,sha256=hJKcH-NbgWK6fmK7f3qex7ozJJl-PqCNPXqpwfcHwJg,22707
-biopipen/scripts/tcr/Attach2Seurat.R,sha256=kJck_jpjpLhUx1_9vjBeKWCrzI8Gb09nGwUOtp1Ztnk,1315
-biopipen/scripts/tcr/CDR3AAPhyschem.R,sha256=p5vBspsd0H3xgk2iptjbGlxfJZlW16BIy3lVcwiMfEI,16656
+biopipen/scripts/tcr/Attach2Seurat.R,sha256=C91TAh1cLSxWkdFPf84pbxlpTYMuWq_rduG4eiIkXZI,1345
+biopipen/scripts/tcr/CDR3AAPhyschem.R,sha256=rvXa9z7EY745Su0bzz0WpBd6QxXMGrzV_Eq7Ur9xb_g,16645
 biopipen/scripts/tcr/CloneResidency.R,sha256=sH76jRg_5q0THsIlgcHMCucdQyeLsc4jixbF938ennI,21421
 biopipen/scripts/tcr/CloneSizeQQPlot.R,sha256=5FPfWQjxTsv59KSDQaDWj3C95zPQMngKG7qOf95NEzI,4527
 biopipen/scripts/tcr/GIANA/GIANA.py,sha256=0qLhgCWxT8K-4JvORA03CzBPTT5pd4Di5B_DgrHXbFA,47198
@@ -163,15 +168,15 @@ biopipen/scripts/tcr/Immunarch-overlap.R,sha256=6RxXTjGhWzUC_1BxojMFrbrTq2PI_EAo
 biopipen/scripts/tcr/Immunarch-spectratyping.R,sha256=ICmCbsUDvwYjwL9kTiTEqQ7Fpmy7t7_GAJ5VTU9IeOU,2977
 biopipen/scripts/tcr/Immunarch-tracking.R,sha256=j1w36v1YuzohW1Nd14m90wRtjzpJSD6OM5KbF_wVxcY,4443
 biopipen/scripts/tcr/Immunarch-vjjunc.R,sha256=nOueF9l4_KVrKSZ1Sl0yObmjbd-5Hms2-RON6K23idg,3736
-biopipen/scripts/tcr/Immunarch.R,sha256=wddxHA4mGAdlQ_P7IXEiovVFYDTb9buGyFQ1MwwEHjI,2943
+biopipen/scripts/tcr/Immunarch.R,sha256=L8rGJ4GODQ-anB8aIVmlPqRK01FBLhw6_ANT_4L6jhU,3030
 biopipen/scripts/tcr/Immunarch2VDJtools.R,sha256=QB9ILGbnsfoWaRANK6ceb14wpSWy8F1V1EdEmfIqiks,706
 biopipen/scripts/tcr/ImmunarchFilter.R,sha256=o25O36FwH_0w6F8DFQ0SfpcwDzlzaGefXqr9ESrvb4k,3974
-biopipen/scripts/tcr/ImmunarchLoading.R,sha256=vg3Pg_5JvcOiT3gOrWn98EpjGi8r7SYh52hhvfSyyzk,5836
+biopipen/scripts/tcr/ImmunarchLoading.R,sha256=BNUJorjfF2R-j2ApUFKrAgqAJxzhzsDN9RUqzpkrfDY,5426
 biopipen/scripts/tcr/ImmunarchSplitIdents.R,sha256=FGCeGV0uSmFU91lKkldUAeV4A2m3hHw5X4GNi8ffGzI,1873
 biopipen/scripts/tcr/SampleDiversity.R,sha256=jQ1OU3b8vswD8tZhLt3fkcqJKrl2bhQX0giHM2rXz3Y,2643
 biopipen/scripts/tcr/TCRClusterStats.R,sha256=3YxIfsTBbFFI6fBTU3gM60bGuVv52PmL7bs16_WciGw,12089
-biopipen/scripts/tcr/TCRClustering.R,sha256=yfIiCMQuywjoJnAXwRJjlJsoYIA8swUMKIt_AsGvHQY,8566
-biopipen/scripts/tcr/TESSA.R,sha256=math-ZvkxYlZvXuHB0dNz3sv8hkx7p87EFW2PmEvJ60,7294
+biopipen/scripts/tcr/TCRClustering.R,sha256=bW9cwVZCRlFIqO03LsUKu6qk6xZ_WxarHDUcnl_diT8,8592
+biopipen/scripts/tcr/TESSA.R,sha256=nvzkhJHziTOjgZvAuU0L6qqCNgSp9f90P0i4tEMivwA,6798
 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
@@ -200,20 +205,20 @@ biopipen/scripts/vcf/VcfSplitSamples.py,sha256=GraKi7WluzDAvVVGljwd3Yif6MriniF8s
 biopipen/scripts/web/Download.py,sha256=WKC_t5ZEeJoKFyY9XwksHARcMbKmHMcxNEUDLMGJ0Cc,924
 biopipen/scripts/web/DownloadList.py,sha256=cZvdi3LVzlATiTvAXe0uuDDXGqB5jcR2zHrMLCEb2U8,1130
 biopipen/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biopipen/utils/common_docstrs.py,sha256=7jnUhJ0GKV9YR6-wZYqycenGoQIz8Nol5auhKYuIGMM,3060
+biopipen/utils/common_docstrs.py,sha256=77whqrhTg6kA7XHW5s7RJT3tGLo-d0XzgPc3LriBdgI,3296
 biopipen/utils/gene.R,sha256=BzAwlLA8hO12vF-3t6IwEuTEeLa_jBll4zm_5qe3qoE,1243
 biopipen/utils/gene.py,sha256=qE_BqTayrJWxRdniffhcz6OhZcw9GUoOrj2EtFWH9Gw,2246
 biopipen/utils/gsea.R,sha256=o3RC-wejsfFXPXzRIpFw22F-aif27qnuKEPavvXIlkc,5794
 biopipen/utils/io.R,sha256=jIYdqdn0iRWfQYAZa5CjXi3fikqmYvPPLIXhobRe8sw,537
 biopipen/utils/misc.R,sha256=nkjiAsEsilq0AeiKRDNqrhTx-1Grqg-rFlkjOEOEDYg,5224
 biopipen/utils/misc.py,sha256=Pmh3CBiKJ3vC_RqorfOfRAvTVKXrGDJT8DMLfYbTivs,3055
-biopipen/utils/mutate_helpers.R,sha256=E4OcaMC7aqb6D6m3dXSDLdHhTZb8RUksjtFwHweMGF8,13219
+biopipen/utils/mutate_helpers.R,sha256=F_DYYjmmlPp2FppNIFUI1cNKsR2vUCwDn7NlvinasBQ,13068
 biopipen/utils/plot.R,sha256=pzl37PomNeUZPxohHZ2w93j3Fc4T0Qrc62FF-9MTKdw,4417
 biopipen/utils/reference.py,sha256=6bPSwQa-GiDfr7xLR9a5T64Ey40y24yn3QfQ5wDFZkU,4420
 biopipen/utils/rnaseq.R,sha256=Ro2B2dG-Z2oVaT5tkwp9RHBz4dp_RF-JcizlM5GYXFs,1298
 biopipen/utils/single_cell.R,sha256=bKduqOQjSC8BtZJuwfUShR49omoEMbB57n3Gi6dYlqA,4147
 biopipen/utils/vcf.py,sha256=ajXs0M_QghEctlvUlSRjWQIABVF02wPdYd-0LP4mIsU,9377
-biopipen-0.22.0.dist-info/METADATA,sha256=Qc13J8hjCs_d1_nhm5emj93Knx889HqPT7ciqRVlKjQ,886
-biopipen-0.22.0.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-biopipen-0.22.0.dist-info/entry_points.txt,sha256=sfI6oDEEuMvAg0KNujE9uu-c29y7IwQQA1_A2sUjPhc,527
-biopipen-0.22.0.dist-info/RECORD,,
+biopipen-0.22.2.dist-info/METADATA,sha256=vtGP0R0JZ3mSaEgRjhGbqNuLnbmYp1Rc7XoErM1JCxo,886
+biopipen-0.22.2.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
+biopipen-0.22.2.dist-info/entry_points.txt,sha256=-rKo4gInvzqlh7_2oEVmEo9gKO9y1ba3rHWTWOM5xP4,561
+biopipen-0.22.2.dist-info/RECORD,,

{biopipen-0.22.0.dist-info → biopipen-0.22.2.dist-info}/entry_points.txt

@@ -2,6 +2,7 @@
 bam=biopipen.ns.bam
 bcftools=biopipen.ns.bcftools
 bed=biopipen.ns.bed
+cellranger=biopipen.ns.cellranger
 cnv=biopipen.ns.cnv
 cnvkit=biopipen.ns.cnvkit
 cnvkit_pipeline=biopipen.ns.cnvkit_pipeline