Discover and read the best of Twitter Threads about #nullranges
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excluderanges is a Bioconductor data resource providing sets of problematic genomic regions (previously, "blacklisted"). It covers six organisms, 12 genome assembles, and new exclusion sets for mouse mm39 and human telomere-to-telomere (T2T) genomes. doi.org/10.1101/2022.1… 
Most exclusion sets from ENCODE, UCSC Genome Browser, GitHub lack curation methods. We uniformly processed and annotated 84 exclusion sets and made them available on AnnotationHub and via the BEDbase.org API. Tutorial at dozmorovlab.github.io/excluderanges/
For hg38, @anshulkundaje recommends 'GRCh38_unified_blacklist.bed' , also the most comprehensive and annotated in our tests. We also recommend explicitly combining exclusion sets with centromeres, telomeres, short arm gap regions.
Eric Davis @ericscottdavis1 & Wancen Mu @WancenM presenting two branches of functionality in the {nullranges} pkg: finding matched sets of genomic ranges based on covariates & bootstrapping blocks of genomic ranges. Both play well w/ {plyranges} for downstream analysis
#bioc2022
#bioc2022
Both methods are based statistical methods for refining null comparisons. E.g. we were inspired by {MatchIt}, {cobalt} and other matching packages, as well as {GSC} for the block bootstrap (method described in Bickel et al 2010)
Development and conference attendance for Eric and Wancen was supported by an EOSS award from @cziscience. Contributions from @dphansti, @mikhaildozmorov, @_StuartLee, @timtriche and other members of #nullranges slack channel
Previously described here:
Previously described here:
This #EOSS funding from @cziscience for #DESeq2 and #tximeta wrapped up at the end of 2021.
Reporting in this 🧵 on what we developed:
Reporting in this 🧵 on what we developed:
1. @kwame_forbes wrote DESeq2::integrateWithSingleCell() which helps user locate publicly available SC datasets followed by visualization with his own R package:
kwameforbes.github.io/vizWithSCE/
Kwame was then a @UNCPREP scholar, now a first year BCB student at UNC 🧬💻🎉
kwameforbes.github.io/vizWithSCE/
Kwame was then a @UNCPREP scholar, now a first year BCB student at UNC 🧬💻🎉
2. Some Bioc folks and a team at UNC worked on extending the tximeta + DESeq2 + plyranges workflow that @_StuartLee @lawremi and I started in the fluentGenomics paper:
sa-lee.github.io/fluentGenomics/
sa-lee.github.io/fluentGenomics/
