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.

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/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