Release Notes#

Release 2.7.1 (released October 29, 2024)#

Features:#

  • Implement barcode correction algorithms.

  • Add smooth_length to ex.export_coverage.

Bugs fixed:#

  • Fix #335: GTF parsing error when textual attributes contain semicolons.

  • Fix #347: Add file name sanity check in various places.

Release 2.7.0 (released August 27, 2024)#

Features:#

  • Return more QC metrics from pp.make_fragment_file.

  • Also compute library-level TSSe in metrics.tsse.

  • pp.make_fragment_file can now work with 10X BAM files by specifying source=10x.

  • Add pp.call_cells to identify nonempty barcodes from raw data.

  • Add pp.recipe_10x_metrics to compute 10X metrics.

  • Add pp.import_contacts to process scHi-C data.

  • Implement pseudo-bulk peak calling in tl.macs3.

Other Changes:#

  • Change the default counting strategy from “insertion” to “paired-insertion” in pp.add_tile_matrix, pp.make_peak_matrix, pp.make_gene_matrix.

  • Minor changes in TSSe calculation.

Release 2.6.4 (released May 28, 2024)#

Features:#

  • Implement #304: Add some flexibility to pp.make_gene_matrix by allowing the user to change upstream and downstream distances for TSS calculation.

  • Other minor improvements.

Release 2.6.3 (released May 15, 2024)#

Bugs fixed:#

  • Fixed external sorter issues in version 2.6.2.

Release 2.6.2 (released May 9, 2024)#

Features:#

  • Add the argument exclude_chroms to metrics.tsse to exclude certains chromosomes from TSSe calculation. The default is “chrM”.

Release 2.6.1 (released May 2, 2024)#

Features:#

  • Add the argument inplace to AnnData subset function. As a result, if you want to perform out-of-place subset, you need to set inplace=False explicitly. Before you just need to set the out parameter. The benefit of this change is that you can save the subset in memory by setting out=None, inplace=False, which cannot be achieved before.

  • Use only the unique TSSs instead of all TSSs read from the GTF file in metrics.tsse calculation.

Bugs fixed:#

  • Fix #252: tl.spectral does not raise an error when the input matrix is in compressed column format, whereas it should expect a compressed sparse row format.

  • Fix a bug in pp.import_data which produces incorrect duplication rates when the input data contains mitochondrial reads.

Release 2.6.0 (released March 9, 2024)#

Features:#

  • Add a argument counting_strategy to pp.add_tile_matrix, pp.make_peak_matrix, and pp.make_gene_matrix, which allows one to use different strategies (insertion-based, fragment-based, or paired insertion counting) to compute feature counts.

  • Fix #233: Add Apple silicon wheel files.

Bugs fixed:#

  • Fix #221: ‘pp.knn’ with ‘method=pynndescent’ invalid csr matrix.

  • Fix #226: Backed AnnData does not support numpy string array.

  • Fix #232: tempdir is not respected in tl.macs3.

  • Fix #242: Change default value of min_len to extsize in tl.macs3, in order to be consistent with the macs3 command line tool.

  • Other minor bug fixes.

Release 2.5.3 (released Jan 16, 2024)#

Features:#

  • Add count_frag_as_reads argument to pp.make_tile_matrix, pp.make_peak_matrix, and pp.make_gene_matrix.

Bugs fixed:#

  • Fix: ex.export_coverage generates empty files in v2.5.2.

Release 2.5.2 (released Jan 4, 2024)#

Features:#

  • Support anndata v0.10.

  • Make it easier to build custom genome objects.

  • Allow customized “gene_id” and “gene_name” keys in pp.make_gene_matrix.

  • Add ex.export_coverage to export coverage tracks as bedGraph or bigWig files. This deprecates ex.export_bigwig.

  • Add read_10x_mtx to read 10X mtx files.

  • Implement #192: filtering fragments by size before quantification. This adds min_frag_size and max_frag_size parameters to pp.add_tile_matrix, pp.make_peak_matrix, and pp.make_gene_matrix.

Bugs fixed:#

  • Fix a bug in pp.add_tile_matrix that causes the function to fail when the genome contains a large number (>1000) of chromosomes.

  • Fix memory leak in tl.macs3.

  • Fix #177: counter overflow in pp.make_fragment_file when duplicate reads are more than 2^16.

  • Fix #178: issue a warning instead of an error when no cells pass the filter in pp.import_data.

  • Fix #179: AnnDataSet to AnnData conversion error when .X is empty.

  • Fix #182: compression type detection problem.

Release 2.5.1 (released Oct 23, 2023)#

Function renaming:#

  • ex.export_bed is renamed to ex.export_fragments.

Features:#

  • Add zstandard file support at various places.

  • Change the default output format of ex.export_bed to zst. To restore the old behavior, set suffix='.bed.gz'.

Bugs fixed:#

  • Fix a bug in pp.import_data that causes the function to occasionally fail on small chunk sizes.

Release 2.5.0 (released Oct 10, 2023)#

Breaking changes:#

  • Fragments are now stored in .obms['fragment_single'] or .obsm['fragment_paired'], depending on whether the data is single-end or paired-end. As a result, the h5ad files generated prior to this version are no longer compatible.

  • tl.call_peaks has been renamed to tl.macs3, and the underlying algorithm has been significantly improved, see #142. tl.macs3 doesn’t automatically merge returned peaks anymore. Use tl.merge_peaks to merge peaks. Please read the updated tutorial for more details.

  • pp.import_data now doesn’t compute the TSS enrichment scores. Use metrics.tsse to compute the TSS enrichment scores. genome parameter is renamed to chrom_sizes.

Features:#

  • Add tl.merge_peaks to perform peak merging.

  • Allow using custom mitochondrial chromosome names in pp.import_data.

  • Change the default algorithm in pp.knn to kd-tree.

Bugs fixed:#

  • #165: Fix reproducibility issues in various functions.

Release 2.4.0 (released Sep 12, 2023)#

Features:#

  • Add multiprocessing support to various preprocessing functions like pp.import_data.

  • Add experimental pp.import_contacts to import scHi-C data.

  • Add pp.scanorama_integrate to perform batch correction using Scanorama.

Bugs fixed:#

  • #145, #148, and others.

Release 2.3.1 (released Jun 21, 2023)#

Features:#

  • Add pp.add_frip to calculate the fraction of reads in peaks or other types of feature sets.

  • Make pp.make_fragment_file’s behavior more deterministic.

Bugs fixed:#

  • #119, #127, #131.

Release 2.3.0 (released Apr 14, 2023)#

Breaking changes:#

  • Due to a major upgrade of the anndata-rs package. The AnnData object generated by older versions is no longer compatible with the new version.

  • All dataframes in backed mode are now indexless.

  • The pp.call_doublets and pl.scrublet has been removed. pp.scrublet now automatically calls doublets.

  • Rename the argument gff_file to gene_anno in pp.import_data and pp.make_gene_matrix. Because the gene annotation file is no longer required to be a GFF file.

Features:#

  • Updates to tl.spectral:

    1. Change the default similarity metric to the cosine similarity.

    2. Significantly improve the scalability of the algorithm when using the cosine similarity. Both the time and space complexity are now linear!

    3. The returned eigenvectors are now weighted by eigenvalues so that using the elbow method to select the number of eigenvectors is no longer necessary. To restore the old behavior, set weighted_by_sd=False.

  • Implement tl.multi_spectral to perform dimension reduction on multiple modalities simultaneously.

  • Most preprocessing functions can now take a list of AnnData objects as input, and process them in parallel.

  • pp.make_tile_matrix: allow excluding certain chromosomes by setting exclude_chroms.

Bugs fixed:#

  • Fix a bug in pp.call_doublets that leads to incorrect thresholds for certain datasets.

  • Fix #80, #97, #102, #103, #109, #110.

Release 2.2.0 (released Dec 2, 2022)#

Breaking changes:#

  • create_dataset has been removed. Please use the AnnDataSet constructor to create the AnnDataSet object.

  • Argument storage is renamed to file in a variety of AnnData IO functions, including create_dataset, read_mtx, and read_csv.

  • Argument no_check is removed in read_dataset.

  • mode is renamed to backed in .read().

Features:#

  • Support in-memory AnnData and flexible conversions between backed and in-memory AnnData.

Release 2.1.3 (released Nov 2, 2022)#

Features:#

  • Add a low-memory mode in pp.import_data for parsing large unsorted fragment files.

Bugs fixed:#

  • Minor bug fixes and performance improvements.

  • Fix 10X bam file parsing in pp.make_fragment_file.

Release 2.1.2 (released Oct 1, 2022)#

Bugs fixed:#

  • Minor bug fixes and performance improvements.

Release 2.1.1 (released Sep 28, 2022)#

Features:#

  • Add “tl.motif_enrichment” to perform motif enrichment analysis.

Bugs fixed:#

  • Fix bugs in “ex.export_bigwig”. NOTE: prior to this version, this function does not work as expected. Please update and rerun if you have used this function in 2.1.0.

Release 2.1.0 (released Sep 17, 2022)#

Breaking changes:#

  • “pp.make_tile_matrix” has been renamed to “pp.add_tile_matrix”.

  • “snapatac2.genome” has been redesigned. A new “Genome” class is added for automatic download of gene annotation files. Objects in “snap.genome.*” are now instances of the Genome object.

  • Rename each occurrence of “group_by” to “groupby” to be consistent with other packages.

Features:#

  • Add “tl.diff_test” to identify differentially accessible regions.

  • Add “tl.make_fragment_file” to convert BAM files to fragment files.

  • Add various functions to perform transcriptional regulatory network analysis.

  • Add “read_10x_mtx” for reading files produced by 10X CellRanger pipeline.

  • Add “ex.export_bigwig” to generate bigwig files.

Bugs fixed:#

  • Various bug fixes and performance improvements.

Release 2.0.0 (released Jul 7, 2022)#

This is the first official release of SnapATAC2!

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