26 skills found
arq5x / Bedtools2bedtools - the swiss army knife for genome arithmetic
daler / PybedtoolsPython wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
biowasm / BiowasmWebAssembly modules for genomics
lh3 / CgrangesA C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
arq5x / BedtoolsA powerful toolset for genome arithmetic.
rnabioco / ValrGenome Interval Arithmetic in R
arq5x / Bedtools ProtocolsNo description available
noamteyssier / Giagia: Genomic Interval Arithmetic
olgabot / Rna Seq Diff ExprnRNA-Sequencing data differential expression analysis pipeline. Performs: genome coverage (via bedtools and HTSeq), generates Circos code and plots, differential expression (via DESeq and NOISeq), structural variant detection (e.g. fusion genes, via SVDetect) and differential exon usage (via DEXSeq).
noamteyssier / Bedrsbedtools-like functionality for interval sets in rust
PhanstielLab / BedtoolsrR package wrapping bedtools
davetang / Defining Genomic RegionsDefine regions in the genome
arq5x / Bedtools PythonA Python interface to the BEDTools API using Cython
MariaNattestad / CopycatCopycat is a simple script to capture and bin the read coverage across a genome from a bam file of read alignments. It relies on bedtools to get coverage for each individual nucleotide in the genome using bedtools genomecov, then bins and organizes these coverage values into 10kb bins and outputs the coverage information in a .csv format (for upload to SplitThreader) and in a .seg format (for viewing the copy number profile in IGV)
rpianezza / GenomeDeltaDetecting transposable element invasions without repeat library. Detects also horizontal transfer events and endogenized viruses. All you need is a reference genome and some short reads
KCCG / SeaveSeave is a web platform that enables genetic variants to be easily filtered and annotated with in silico pathogenicity prediction scores and annotations from popular disease databases. Seave stores genomic variation of all types and sizes, and allows filtering for specific inheritance patterns, quality values, allele frequencies and gene lists. Seave is open source and deployable locally, or on a cloud computing provider, and works readily with gene panel, exome and whole genome data, scaling from single labs to multi-institution scale.
DEIB-GECO / PyGMQLPython Library for data analysis based on GMQL
LBGC-CFB / SpliceLauncherRNAseq pipeline for alternative splicing junctions
milospjanic / RsID2BedrsID2Bed is a script to convert SNP rsIDs to a list of genomics positions in a bed format: chr, position, position+1. Script is useful for quick conversion of SNPs to a bed format for downstream analysis (e.g. overlaps with bedtools).
vinay-swamy / RBedtoolsR wrapper for Bedtools
