ShahCompBio

spectrum-tme

Supporting material for publication: "Ovarian cancer mutational processes drive site-specific immune evasion"

signals

Single Cell Genomes with Allele Specificity

scrna_demultiplexing

TreeAlign

scgenome-deprecated

pypeliner

classifycopynumber

Classify Copy Number Amplifications and Deletions

gdan-sv-consensus

Getting GDAN SV consensus based on bedpe files

igver

Automatically take IGV snapshots

medicc2_nextflow

Medicc2 nextflow pipeline

onboarding

ontmont

ONT split read analysis

scdna_replication_tools

Tools for assigning S-phase cells to clones and inferring single-cell replication timing (scRT) profiles

wgs_analysis

alhena_igo

Alhena loader for IGO

alhenaloader

bulk-illumina-rnaseq

RNA seq analysis pipeline for alignment and quantification of bulk illumina data

bulk-rnaseq

Pipeline for processing bulk RNAseq data

cancer_transcriptional_programs

cell_cycle_classifier

Classifier of cell cycle state from DLP+ data

cellranger_utils

drost-rhabdoids

Analysis of rhabdoid ONT WGS samples from Drost lab

generate_mafs

Generate Variant Tables from Isabl Results

mmctm-pipeline-gdan

MMCTM pipeline for GDAN projects

nanoseq

Nanopore demultiplexing, QC and alignment pipeline

oncokb-annotation

Simple script to annotate variants using oncokb

remixt-postprocess-qc

Make QC plots for ReMixT postprocess `remixt_cn` files

savana-pipeline

SAVANA SV caller pipeline: https://github.com/cortes-ciriano-lab/savana

squamous_cell_analysis

tangent-pipeline

Pipeline for running `tangent` (from Broad Institute)