diff --git a/r/DESCRIPTION b/r/DESCRIPTION index 14dd90c..17faadb 100644 --- a/r/DESCRIPTION +++ b/r/DESCRIPTION @@ -1,12 +1,13 @@ Package: BPCells Title: Single Cell Counts Matrices to PCA -Version: 0.2.0 +Version: 0.3.0 Authors@R: c( person(given = "Benjamin", family = "Parks", role = c("aut", "cre", "cph"), email = "bparks@alumni.stanford.edu", comment = c(ORCID = "0000-0002-0261-7472")), + person("Immanuel", "Abdi", role = "aut"), person("Stanford University", role=c("cph", "fnd")), person("Genentech, Inc.", role=c("cph", "fnd"))) Description: > Efficient operations for single cell ATAC-seq fragments and diff --git a/r/NEWS.md b/r/NEWS.md index 686344d..68180c8 100644 --- a/r/NEWS.md +++ b/r/NEWS.md @@ -1,12 +1,21 @@ # BPCells 1.0 Roadmap - ~~Parallelization~~ (basic support complete. See below) -- Native python library (re-using C++ backend) +- Native python library (re-using C++ backend; basic support started) - Peak-gene correlations -- MACS peak calling +- ~~MACS peak calling~~ (basic support complete. See below) Contributions welcome :) -# BPCells 0.2.1 (main branch - in progress) +# BPCells 0.3.0 (12/21/2024) + +The BPCells 0.3.0 release covers 6 months of changes and 45 commits from 5 contributors. Notable improvements +this release include support for peak calling with MACS and the addition of pseudobulk matrix and stats calculations. +We also released an initial prototype of a BPCells Python library (more details [here](https://bnprks.github.io/BPCells/python/index.html)). +Full details of changes below. + +Thanks to @ycli1995, @Yunuuuu, and @douglasgscofield for pull requests that contributed to this release, as well as to users who +sumitted github issues to help identify and fix bugs. We also added @immanuelazn to the team as a new hire! He is responsible for many +of the new features this release and will continue to help with maintenance and new development moving forwards. ## Features - `apply_by_col()` and `apply_by_row()` allow providing custom R functions to compute per row/col summaries. diff --git a/r/R/atac_utils.R b/r/R/atac_utils.R index 9bd797d..b0b6e90 100644 --- a/r/R/atac_utils.R +++ b/r/R/atac_utils.R @@ -625,7 +625,7 @@ call_peaks_macs <- function(fragments, path, #' @export #' @keywords internal call_macs_peaks <- function(...) { - lifecycle::deprecate_warn("0.2.0", "call_macs_peaks()", "call_peaks_macs()") + lifecycle::deprecate_warn("0.3.0", "call_macs_peaks()", "call_peaks_macs()") return(call_peaks_macs(...)) } diff --git a/r/R/trackplots.R b/r/R/trackplots.R index 357cd3d..998bfec 100644 --- a/r/R/trackplots.R +++ b/r/R/trackplots.R @@ -428,7 +428,7 @@ trackplot_coverage <- function(fragments, region, groups, assert_is(colors, "character") assert_true(length(colors) >= length(unique(groups))) if (!is.null(legend_label)) { - lifecycle::deprecate_warn("0.2.0", "trackplot_coverage(legend_label)", details="Argument value is no longer used since color legend is not shown.") + lifecycle::deprecate_warn("0.3.0", "trackplot_coverage(legend_label)", details="Argument value is no longer used since color legend is not shown.") } groups <- as.factor(groups) @@ -1033,7 +1033,7 @@ trackplot_bulk <- function(fragments, region, groups, legend_label = "group", zero_based_coords = !is(region, "GRanges"), return_data = FALSE, return_plot_list = FALSE, apply_styling = TRUE) { - lifecycle::deprecate_warn("0.2.0", "trackplot_bulk()", "trackplot_combine()") + lifecycle::deprecate_warn("0.2.0", "trackplot_bulk()", "trackplot_coverage()") assert_is(fragments, "IterableFragments") assert_not_null(cellNames(fragments))