Repositories list

• alhena_igo

  Public
  Alhena loader for IGO

  Python

  •

  MIT License

  •0•0•0•1•Updated Dec 20, 2024Dec 20, 2024

• ontmont

  Public
  ONT split read analysis

  Python

  •

  MIT License

  •0•1•0•0•Updated Dec 10, 2024Dec 10, 2024

• gdan-sv-consensus

  Public
  Getting GDAN SV consensus based on bedpe files

  Python

  •0•1•0•0•Updated Dec 10, 2024Dec 10, 2024

• SVChordinator

  Public
  merge, annotate and visualize structural variants

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Dec 2, 2024Dec 2, 2024

• wgs_analysis

  Public
  Python

  •1•1•0•1•Updated Nov 27, 2024Nov 27, 2024

• signals

  Public
  Single Cell Genomes with Allele Specificity

  bioinformaticsrna-seqsingle-cell

  R

  •

  Other

  •1•8•1•1•Updated Nov 24, 2024Nov 24, 2024

• scrna_demultiplexing

  Public
  Python

  •

  MIT License

  •1•4•0•0•Updated Nov 18, 2024Nov 18, 2024

• cellranger_utils

  Public
  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Nov 18, 2024Nov 18, 2024

• doubleTime

  Public
  doubleTime is a method to estimate the timing of whole-genome doubling event(s) on a clone tree using SNVs

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•0•0•Updated Nov 15, 2024Nov 15, 2024

• igver

  Public
  Automatically take IGV snapshots

  automationbioinformaticsigv+ 1bioinformatics-tool

  Python

  •

  MIT License

  •0•1•1•0•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

• 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•1•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

  •713•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

  •82•0•0•0•Updated May 28, 2024May 28, 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•21•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