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  • scatools Public

    Tools for processing scATAC data

    R 1 Other Updated Sep 26, 2024

  • rstudio-img Public

    Dockerfile Updated Aug 28, 2024

  • miloR Public

    Forked from MarioniLab/miloR

    R package implementation of Milo for testing for differential abundance in KNN graphs

    R GNU General Public License v3.0 Updated Jul 29, 2024

  • CRI_bioinformatics_workshop Public

    Forked from crigrants/CRI_bioinformatics_workshop

    Tutorials and code for CRI bioinformatics workshop.

    HTML MIT License Updated Apr 27, 2024

  • openondemandapps Public

    HTML 2 Updated Feb 26, 2024

  • slurmR Public

    Forked from USCbiostats/slurmR

    slurmR: A Lightweight Wrapper for Slurm

    R Other Updated Feb 21, 2024

  • BoneMarrowMap Public

    Forked from andygxzeng/BoneMarrowMap

    A single cell RNA-seq reference map of human hematopoietic development in the bone marrow, with balanced representation of hematopoietic stem and progenitor cells and differentiated populations

    R GNU General Public License v3.0 Updated Feb 21, 2024

  • SComatic Public

    Forked from cortes-ciriano-lab/SComatic

    A tool for detecting somatic variants in single cell data

    Python 1 Other Updated Feb 1, 2024

  • run_numbat Public

    docker for numbat

    Python Updated Feb 1, 2024

  • meta_programs_tirosh Public

    Repo to patch gene names from Tirosh Meta-Programs Paper

    Updated Jul 6, 2023

  • mergebams Public

    Forked from furlan-lab/mergebams

    Command line tool for merging single cell rna-sequencing bams with intelligent tag preservation

    Rust MIT License Updated Jul 2, 2023

  • seurat Public

    Forked from satijalab/seurat

    R toolkit for single cell genomics

    R Other Updated Jun 7, 2023

  • ascat Public

    Forked from VanLoo-lab/ascat

    ASCAT copy number R package

    HTML Updated Jan 10, 2023

  • vcf2maf Public

    Forked from mskcc/vcf2maf

    Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

    Perl Other Updated Nov 7, 2022

  • bsub Public

    Forked from jokergoo/bsub

    Send R code/R scripts/shell commands to LSF cluster without leaving R

    R Other Updated Sep 1, 2022

  • mjz1.github.io Public

    Updated Aug 24, 2022

  • single_cell_pipeline Public

    Forked from shahcompbio/single_cell_pipeline

    Single Cell Analysis Automated Workflow

    Python GNU General Public License v3.0 Updated Jul 11, 2022

  • ArchR Public

    Forked from GreenleafLab/ArchR

    ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

    R MIT License Updated Jun 23, 2022

  • OnClass Public

    Forked from wangshenguiuc/OnClass

    Single cell typing based on cell ontology

    Python 1 MIT License Updated Jun 21, 2022

  • scCNA Public

    Updated May 24, 2022

  • numbat Public

    Forked from kharchenkolab/numbat

    Haplotype-aware CNV analysis in scRNA-Seq

    R Updated May 10, 2022

  • rocker-versioned2 Public

    Forked from rocker-org/rocker-versioned2

    Run current & prior versions of R using docker. rocker/r-ver, rocker/rstudio, rocker/shiny, rocker/tidyverse, and so on.

    Dockerfile GNU General Public License v2.0 Updated Mar 1, 2022

  • cBioPortalData Public

    Forked from waldronlab/cBioPortalData

    Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment

    R Updated Mar 1, 2022

  • scRNAmp Public

    HTML MIT License Updated Nov 9, 2021

  • run_phylo Public

    SK HPF implementation of the phylowgs clonal evolution pipleine

    Perl Updated Nov 8, 2021

  • CICERO Public

    Forked from stjude/CICERO

    CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.

    Perl Other Updated Aug 12, 2021

  • GenVisR Public

    Forked from griffithlab/GenVisR

    Genome data visualizations

    R Creative Commons Zero v1.0 Universal Updated Oct 20, 2017

  • gdc-docs Public

    Forked from majensen/gdc-docs

    Official repository for GDC User Guides in Markdown format

    JavaScript Apache License 2.0 Updated Aug 3, 2016

  • NGS-Tools-GATK Public

    Forked from rdeborja/NGS-Tools-GATK

    A Perl package containing an interface to the GATK suite of tools.

    Perl Updated May 14, 2016

  • pileup2base Public

    Forked from riverlee/pileup2base

    Parse samtools pileup file to get how many bases and what kind of bases are called

    Perl Updated Nov 4, 2015