Pinned Repositories
alleleCount-FixVAF
Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings). Altered so that it clips all reads by n bases to reduce reference bias.
CanVar
Framework based upon ExAC to provide study specific variant frequencies
containers
Bioinformatics containers
FixVAF
Code to remove bias from Isaac aligned data by clipping all reads for variant positions by 5 bases and producing a modified vcf file.
FR
hg38MutSpot
hg39 version of MutSpot
MutSpot
offline_folium
Allows using folium without an internet connection
randomcode
place for some random code
rnaflow
A simple RNA-Seq differential gene expression pipeline using Nextflow
danchubb's Repositories
danchubb/CanVar
Framework based upon ExAC to provide study specific variant frequencies
danchubb/alleleCount-FixVAF
Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings). Altered so that it clips all reads by n bases to reduce reference bias.
danchubb/containers
Bioinformatics containers
danchubb/FixVAF
Code to remove bias from Isaac aligned data by clipping all reads for variant positions by 5 bases and producing a modified vcf file.
danchubb/FR
danchubb/hg38MutSpot
hg39 version of MutSpot
danchubb/MutSpot
danchubb/offline_folium
Allows using folium without an internet connection
danchubb/randomcode
place for some random code
danchubb/rnaflow
A simple RNA-Seq differential gene expression pipeline using Nextflow
danchubb/SigProfilerExtractor
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
danchubb/something-unique
danchubb/TcellExTRECT