8000 Commits · frattalab/PAPA · GitHub

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Commits

Commits on Apr 14, 2025

add zenodo DOI badge
SamBryce-Smith
authored

Commits on Jan 19, 2024

v0.2.0 (#39)
SamBryce-Smith
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Commits on Jan 5, 2022

Script to filter GTF file based on attributes (#29)
SamBryce-Smith
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Commits on Nov 22, 2021

Code to sum expression by pA site, doc updates, various other changes (#28)
SamBryce-Smith
authored

Commits on Oct 26, 2021

Merge pull request #23 from frattalab/filter_tx_by_cond_tpm
SamBryce-Smith
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add filter tx by min mean tpm across conditions script. Option in config
SamBryce-Smith
committed
Merge pull request #22 from frattalab/filter_tx_by_pas
SamBryce-Smith
authored

Commits on Oct 25, 2021

working script to filter transcripts for close atlas or pas motifs
SamBryce-Smith
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Commits on Oct 22, 2021

Commits on Oct 21, 2021

Commits on Oct 18, 2021

add biopython, pyfaidx to conda env. Update PyRanges version
SamBryce-Smith
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Commits on Oct 8, 2021

support for gencode or ensembl ref gtf for gene-type filtering. Check for input containing exon_number column
SamBryce-Smith
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Commits on Sep 13, 2021

add_intron_number refactor to add_region_number - t - 4/5 min! Uses groupby.rank()
SamBryce-Smith
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Commits on Aug 31, 2021

Commits on Aug 26, 2021

Commits on Aug 25, 2021

make starts & ends int64 via assign not PyRanges(gr.as_df())
SamBryce-Smith
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Commits on Aug 24, 2021

forgot to remove nb_cpu arg whoops
SamBryce-Smith
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remove nb_cpu from get_terminal_regions as no speed benefit
SamBryce-Smith
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catch KeyError exon_number assign. Duplicated over grpby for extraction (~5-10s quicker). Duplicated for single_exon filtering (~1 min quicker)
SamBryce-Smith
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set 'other' to isoform_class not match_class...
< 5D39 a class="Box-sc-g0xbh4-0 dqHWhX AuthorAvatar-module__authorHoverableLink--ED3Do prc-Link-Link-85e08" data-muted="true" muted="" href="/frattalab/PAPA/commits?author=SamBryce-Smith" aria-label="commits by SamBryce-Smith" data-hovercard-url="/users/SamBryce-Smith/hovercard">SamBryce-Smith
committed

Commits on Aug 23, 2021

Commits on Aug 20, 2021

classify internal_intron_spliced
SamBryce-Smith
committed

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