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czbiohub-sf/scrnaseq-for-the-99-percent
czbiohub-sf/scrnaseq-for-the-99-percent Public archiveCode accompanying the paper titled, "Single-cell transcriptomics for the 99.9% of species without reference genomes" by Botvinnik et al, 2021
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czbiohub-sf/orpheum
czbiohub-sf/orpheum Public archiveOrpheum (Previously called and published under sencha) is a Python package for directly translating RNA-seq reads into coding protein sequence.
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dissertation
dissertation PublicComputational analysis of single-cell alternative splicing: A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioinformatics and Systems Bi…
488 contributions in the last year
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Activity overview
Contribution activity
February 2025
Created 15 commits in 3 repositories
Created a pull request in seanome/kmerseek that received 47 comments
Initial commit of kmerseek search, index
This PR implements what was originally in the fairly messy notebooks: https://github.com/olgabot/botryllus-mhc/blob/main/notebooks/201_create_all_…
Opened 3 other pull requests in 3 repositories
seanome/kmerseek
1
open
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Separate "index" and "search" into substeps for nextflow pipeline
This contribution was made on Feb 25
seanome/2025-biodata-wealth-inequality
1
open
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olgabot/pdb uniprot swissprot trembl all predicted
This contribution was made on Feb 18
olgabot/botryllus-mhc
1
open
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olgabot/yc demo prep
This contribution was made on Feb 5
Reviewed 2 pull requests in 2 repositories
seanome/kmerseek
1 pull request
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Initial commit of kmerseek search, index
This contribution was made on Feb 26
sourmash-bio/sourmash_plugin_branchwater
1 pull request
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Documentation update:
manysketch --force
allows use of FASTA files in more than one sketchThis contribution was made on Feb 8
Created an issue in seanome/kmerseek that received 2 comments
Parallelize sourmash sig kmers
!
sourmash sig kmers
(wrapped in kmerseek.sketch.get_kmers
called by kmerseek.entity.KmerseekEntity
) is a single-threaded process that merges the pro…
Opened 7 other issues in 1 repository
seanome/kmerseek
7
open
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Split "kmerseek search" into "search-create-query-sketch", "search-get-query-kmers", "search-do-search", "search-get-matching-kmers"
This contribution was made on Feb 14
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Split "kmerseek index" into "index-create-sketch", "index-get-kmers", "index-rocksdb"
This contribution was made on Feb 14
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Get Uniprot domains from overlapping regions found in k-mers
This contribution was made on Feb 11
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Move adding start position to kmers into "sourmash sig kmers"
This contribution was made on Feb 11
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Figure out why "manysearch" and "multisearch" aren't working with rocksdbs
This contribution was made on Feb 11
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Actually test the contents of the "kmerseek index" output
This contribution was made on Feb 11
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Benchmark "sourmash scripts multisearch" vs "sourmash scripts manysearch" + polars-based TF-IDF/probability of overlap calculation
This contribution was made on Feb 11