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    132 repositories

    • signals

      Public
      Single Cell Genomes with Allele Specificity
      bioinformaticsrna-seqsingle-cell
      R
      •
      Other
      •1•8•1•0•Updated Nov 12, 2024Nov 12, 2024

    • igver

      Public
      Automatically take IGV snapshots
      automationbioinformaticsigvbioinformatics-tool
      Python
      •
      MIT License
      •0•1•1•0•Updated Nov 11, 2024Nov 11, 2024

    • doubleTime

      Public
      doubleTime is a method to estimate the timing of whole-genome doubling event(s) on a clone tree using SNVs
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•1•Updated Nov 11, 2024Nov 11, 2024

    • wgs

      Public
      Whole genome workflows
      Python
      •6•12•0•0•Updated Nov 9, 2024Nov 9, 2024

    • pypeliner

      Public
      Python
      •
      GNU General Public License v3.0
      •5•2•0•0•Updated Oct 16, 2024Oct 16, 2024

    • wgs_analysis

      Public
      Python
      •1•1•0•1•Updated Oct 3, 2024Oct 3, 2024

    • ontmont

      Public
      ONT split read analysis
      Python
      •
      MIT License
      •0•1•0•0•Updated Oct 2, 2024Oct 2, 2024

    • alhena_igo

      Public
      Alhena loader for IGO
      Python
      •
      MIT License
      •0•0•0•1•Updated Sep 26, 2024Sep 26, 2024

    • alhenaloader

      Public
      Python
      •
      MIT License
      •0•0•0•1•Updated Sep 26, 2024Sep 26, 2024

    • scdna_replication_paper

      Public
      Investigating DNA replication dynamics using DLP data
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 31, 2024Jul 31, 2024

    • scdna_replication_tools

      Public
      Tools for assigning S-phase cells to clones and inferring single-cell replication timing (scRT) profiles
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Jul 29, 2024Jul 29, 2024

    • medicc2_nextflow

      Public
      Medicc2 nextflow pipeline
      Nextflow
      •1•1•0•2•Updated Jul 25, 2024Jul 25, 2024

    • bulk-illumina-rnaseq

      Public
      RNA seq analysis pipeline for alignment and quantification of bulk illumina data
      Nextflow
      •
      MIT License
      •705•0•0•0•Updated Jun 29, 2024Jun 29, 2024

    • generate_mafs

      Public
      Generate Variant Tables from Isabl Results
      Python
      •1•0•0•0•Updated Jun 27, 2024Jun 27, 2024

    • oncokb-annotation

      Public
      Simple script to annotate variants using oncokb
      Shell
      •0•0•0•0•Updated May 31, 2024May 31, 2024

    • nanoseq

      Public
      Nanopore demultiplexing, QC and alignment pipeline
      Nextflow
      •
      MIT License
      •80•0•0•0•Updated May 28, 2024May 28, 2024

    • scrna_demultiplexing

      Public
      Python
      •
      MIT License
      •1•4•0•0•Updated May 21, 2024May 21, 2024

    • gdan-sv-consensus

      Public
      Getting GDAN SV consensus based on bedpe files
      Python
      •0•1•0•0•Updated Apr 19, 2024Apr 19, 2024

    • cellranger_utils

      Public
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Apr 18, 2024Apr 18, 2024

    • onboarding

      Public
      1•1•0•0•Updated Apr 15, 2024Apr 15, 2024

    • scgenome-deprecated

      Public
      Jupyter Notebook
      •4•3•6•9•Updated Mar 28, 2024Mar 28, 2024

    • savana-pipeline

      Public
      SAVANA SV caller pipeline: https://github.com/cortes-ciriano-lab/savana
      Python
      •0•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • drost-rhabdoids

      Public
      Analysis of rhabdoid ONT WGS samples from Drost lab
      Python
      •0•0•0•0•Updated Jan 18, 2024Jan 18, 2024

    • mmctm-pipeline-gdan

      Public
      MMCTM pipeline for GDAN projects
      Python
      •0•0•0•0•Updated Jan 9, 2024Jan 9, 2024

    • cell_cycle_classifier

      Public
      Classifier of cell cycle state from DLP+ data
      Python
      •
      MIT License
      •1•0•0•7•Updated Jan 9, 2024Jan 9, 2024

    • TreeAlign

      Public
      Jupyter Notebook
      •0•4•3•0•Updated Dec 22, 2023Dec 22, 2023

    • bulk-rnaseq

      Public
      Pipeline for processing bulk RNAseq data
      Shell
      •0•0•0•0•Updated Oct 18, 2023Oct 18, 2023

    • spectrum-tme

      Public
      Supporting material for publication: "Ovarian cancer mutational processes drive site-specific immune evasion"
      R
      •8•19•1•0•Updated Sep 14, 2023Sep 14, 2023

    • tangent-pipeline

      Public
      Pipeline for running `tangent` (from Broad Institute)
      Python
      •0•0•0•0•Updated Sep 14, 2023Sep 14, 2023

    • remixt-postprocess-qc

      Public
      Make QC plots for ReMixT postprocess `remixt_cn` files
      Jupyter Notebook
      •0•0•0•0•Updated Sep 1, 2023Sep 1, 2023