All pull requests

Pull requests

• Same SCT normalization for merge and integration in the spatial v5 combine tool, plus DE tool fixes

  #143·mlehtiva opened Nov 12, 2026Contributor·

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• 1-3: Add chr to VCF chromosome names in addChrToVCF

  #140·hupponen opened Nov 5, 2026Contributor·

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• 2.1-13: Regress out the cell cycle in the RNA assay in Seurat v5 merge

  #138·hupponen opened Nov 3, 2026Contributor·

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• 2.1-7: Write the spatially variable genes of all samples to the table

  #137·hupponen opened Nov 3, 2026Contributor·

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• 2.1-10: Return mothur's precluster names file and summarize with the count table

  #136·hupponen opened Nov 3, 2026Contributor·

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• 2.1-12: Give DEXSeq the count files in the phenodata order

  #135·hupponen opened Nov 3, 2026Contributor·

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• 2.1-19: Stop the paired-end HISAT2 and STAR tools unless given exactly two FASTQ files

  #134·hupponen opened Nov 3, 2026Contributor·

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• 1-7: Blame memory in runExternal only for programs killed by a signal

  #133·hupponen opened Nov 2, 2026Contributor·

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• 4-13: Resolve the host name, not the whole netloc, in download-file

  #132·hupponen opened Nov 2, 2026Contributor·

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• 4-7: Fix the protfilter mass filters and the gzipped input

  #130·hupponen opened Nov 2, 2026Contributor·

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• 4-2: Search the full query when the BLAST query location is empty

  #129·hupponen opened Nov 2, 2026Contributor·

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• 4-1: Fix the input file name in fdnadist and fdnaml

  #128·hupponen opened Nov 2, 2026Contributor·

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• 2.2-27: Fix the Dimont delete switch and duplicate logo outputs

  #120·hupponen opened Oct 26, 2026Contributor·

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• 2.2-1: Fix fastq-filter output names, summary separator and name collisions

  #118·hupponen opened Oct 26, 2026Contributor·

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• 2.2-17: Print violin plots in Seurat extract cluster tools

  #109·hupponen opened Oct 14, 2026Contributor·

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• 2.1-6: Plot the last page of split feature plots in split dot plot

  #108·hupponen opened Oct 14, 2026Contributor·

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• 2.2-23: Fix Define NGS experiment crash with a single sample file

  #107·hupponen opened Oct 14, 2026Contributor·

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• 2.2-11: Honour the RPKM saturation parameter in RSeQC quality metrics

  #106·hupponen opened Oct 14, 2026Contributor·

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• 2.2-12: Use the own BED file in RSeQC strandedness inference with a provided genome

  #105·hupponen opened Oct 14, 2026Contributor·

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• 2.2-20: Allow Cufflinks de novo assembly without a GTF

  #104·hupponen opened Oct 14, 2026Contributor·

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• 2.2-2: Fix the Bowtie2 "Fast local" alignment strategy by renaming its option to --fast-local

  #103·hupponen opened Oct 14, 2026Contributor·

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• 2.2-5: Return the BEDPE output of Overlap BEDPE with BED for BAM input

  #101·hupponen opened Oct 14, 2026Contributor·

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• 2.2-6: Fix Coverage BED to report coverage on the intervals in B

  #100·hupponen opened Oct 14, 2026Contributor·

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• 2.2-29: Fix annotate-ensembl-ids header for row names with an ensembl_id column

  #99·hupponen opened Oct 14, 2026Contributor·

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• 2.2-26: Only pass -derep_min to prinseq when it is set

  #98·hupponen opened Oct 14, 2026Contributor·

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