Humam Siga's repositories
BSseq2
Analysing whole genome BS and hBS sequencing data
copycat
Copycat 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)
cue
Deep learning framework for SV calling and genotyping
grocsvs
Genome-wide reconstruction of complex structural variants
MacOSX-Improved-Swedish-Keyboard-Layout
My personal improved keyboard layout for Mac OS X.
MutScape
Ａ user-friendly Python toolkit, which provides a comprehensive pipeline to easily explore the cohort-based mutational characterization for studying cancer genomics.
TitanCNA_10X_snakemake
Snakemake workflow for 10X Genomics WGS analysis using TitanCNA