Pinned Repositories
cellscape
Visualization tool for integrating single cell phylogeny with genomic content to clearly display evolutionary progression and tumour heterogeneity.
hmmcopy_utils
Tools for extracting read counts and gc and mappability statistics in preparation for running HMMCopy.
MultiModalMuSig.jl
A Julia package for extracting mutation signatures using topic models
mutationseq
Software for somatic SNV detection using next generation sequencing (NGS) data.
SCRNApipeline
Single Cell RNA-seq Pipeline
scvis
Python package for dimension reduction of high-dimensional biological data.
single_cell_pipeline
Single Cell Analysis Automated Workflow
spectrum-tme
Supporting material for publication: "Ovarian cancer mutational processes drive site-specific immune evasion"
timescape
Visualization tool for temporal clonal evolution.
wgs
Whole genome workflows
ShahCompBio's Repositories
shahcompbio/spectrum-tme
Supporting material for publication: "Ovarian cancer mutational processes drive site-specific immune evasion"
shahcompbio/signals
Single Cell Genomes with Allele Specificity
shahcompbio/scrna_demultiplexing
shahcompbio/TreeAlign
shahcompbio/scgenome-deprecated
shahcompbio/pypeliner
shahcompbio/doubleTime
doubleTime is a method to estimate the timing of whole-genome doubling event(s) on a clone tree using SNVs
shahcompbio/gdan-sv-consensus
Getting GDAN SV consensus based on bedpe files
shahcompbio/igver
Automatically take IGV snapshots
shahcompbio/medicc2_nextflow
Medicc2 nextflow pipeline
shahcompbio/onboarding
shahcompbio/ontmont
ONT split read analysis
shahcompbio/scdna_replication_tools
Tools for assigning S-phase cells to clones and inferring single-cell replication timing (scRT) profiles
shahcompbio/wgs_analysis
shahcompbio/scdna_replication_paper
Investigating DNA replication dynamics using DLP data
shahcompbio/alhena_igo
Alhena loader for IGO
shahcompbio/alhenaloader
shahcompbio/bulk-illumina-rnaseq
RNA seq analysis pipeline for alignment and quantification of bulk illumina data
shahcompbio/bulk-rnaseq
Pipeline for processing bulk RNAseq data
shahcompbio/cell_cycle_classifier
Classifier of cell cycle state from DLP+ data
shahcompbio/cellranger_utils
shahcompbio/drost-rhabdoids
Analysis of rhabdoid ONT WGS samples from Drost lab
shahcompbio/generate_mafs
Generate Variant Tables from Isabl Results
shahcompbio/mmctm-pipeline-gdan
MMCTM pipeline for GDAN projects
shahcompbio/nanoseq
Nanopore demultiplexing, QC and alignment pipeline
shahcompbio/oncokb-annotation
Simple script to annotate variants using oncokb
shahcompbio/remixt-postprocess-qc
Make QC plots for ReMixT postprocess `remixt_cn` files
shahcompbio/savana-pipeline
SAVANA SV caller pipeline: https://github.com/cortes-ciriano-lab/savana
shahcompbio/squamous_cell_analysis
shahcompbio/tangent-pipeline
Pipeline for running `tangent` (from Broad Institute)