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seq2science

integration_instructionsResearch softwarekeyboard_double_arrow_right Software 11 Dec 2020Publisher:Zenodo
Authors: Van Der Sande, Maarten; Frölich, Siebren; Smits, Jos; Schäfers, Tilman; Snabel, Rebecca; Van Heeringen, Simon;

doi: 10.5281/zenodo.7267813 , 10.5281/zenodo.6504438 , 10.5281/zenodo.6656467 , 10.5281/zenodo.8319140 , 10.5281/zenodo.5358401 , 10.5281/zenodo.6535586 , 10.5281/zenodo.6327277 , 10.5281/zenodo.7594767 , 10.5281/zenodo.4316985 , 10.5281/zenodo.8146679 , 10.5281/zenodo.4658289 , 10.5281/zenodo.5788729 , 10.5281/zenodo.3921913 , 10.5281/zenodo.4748528 , 10.5281/zenodo.7851762 , 10.5281/zenodo.6034404 , 10.5281/zenodo.10137648 , 10.5281/zenodo.10619482 , 10.5281/zenodo.15411299 , 10.5281/zenodo.5577068 , 10.5281/zenodo.4577246 , 10.5281/zenodo.5948679 , 10.5281/zenodo.4451349 , 10.5281/zenodo.6806294 , 10.5281/zenodo.4317342 , 10.5281/zenodo.6536205 , 10.5281/zenodo.5773861 , 10.5281/zenodo.6594512 , 10.5281/zenodo.5078126 , 10.5281/zenodo.4469402 , 10.5281/zenodo.5579087 , 10.5281/zenodo.7990292 , 10.5281/zenodo.8343776 , 10.5281/zenodo.8146692 , 10.5281/zenodo.4360759 , 10.5281/zenodo.6656466 , 10.5281/zenodo.4545622 , 10.5281/zenodo.4897235 , 10.5281/zenodo.8146530 , 10.5281/zenodo.5788720 , 10.5281/zenodo.8185688 , 10.5281/zenodo.6504433 , 10.5281/zenodo.7040780 , 10.5281/zenodo.8361102 , 10.5281/zenodo.7851729 , 10.5281/zenodo.7990412 , 10.5281/zenodo.15412118 , 10.5281/zenodo.7501694

Abstract

Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Changed all conda environments now work with strict channel priorities singlecellTK environment updated (no longer needs pip) increased expected RAM usage of scRNA-seq rule sctk_qc Fixed outdated dependency in scRNA-seq rule export_sce_obj error in singlecellTK script with negative count values in reportCellQC() softmask_track_1 should no longer hang indefinetly On UCSC assembly hubs, the softmask track should align better (fixed off-by-1) upsetplot environment being broken (matplotlib version pinned) deeptools environment being broken (matplotlib version pinned)

Related Organizations
Keywords

snakemake, rna-seq, ngs, atac-seq, reproducible-research, bioinformatics, bioinformatics-pipeline, chip-seq

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    influence
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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
5
Top 10%
Average
Average
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