msk-access/postprocessing_variant_calls

This repository helps with processing for variant calls made by a given caller

Language: Python - Size: 1.41 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 0 - Forks: 2

msk-access/genomenexus_annotation-pipeline

Language: Dockerfile - Size: 1.95 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

msk-access/mutect1

Language: Shell - Size: 9.01 MB - Last synced: 3 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

msk-access/vardict-java

Size: 1000 Bytes - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

msk-access/genotype_variants

Project to genotype SNV, INDEL and SV.

Language: Python - Size: 164 KB - Last synced: 29 days ago - Pushed: 3 months ago - Stars: 1 - Forks: 4

msk-access/mutect1new

Language: Dockerfile - Size: 9.01 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

msk-access/DeltaMSI Fork of RADar-AZDelta/DeltaMSI

DeltaMSI: AI-based screening for microsatellite instability in solid tumors

Language: Python - Size: 91.8 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

msk-access/athena Fork of eastgenomics/athena

Provides HTML reports with detailed coverage analysis for clinical NGS data.

Language: Python - Size: 31.7 MB - Last synced: 6 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

msk-access/PyVCF Fork of jamescasbon/PyVCF

A Variant Call Format reader for Python.

Language: Python - Size: 1.62 MB - Last synced: 6 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

msk-access/resources

Resource files for running MSK-ACCESS workflows

Size: 2.26 MB - Last synced: 9 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 1

msk-access/docker_trim_galore

Dockerized Trim Galore

Language: Dockerfile - Size: 6.84 KB - Last synced: 9 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

msk-access/msk-access.github.io

Documentation for MSK-ACCESS workflows

Language: JavaScript - Size: 1.33 MB - Last synced: 9 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 1

msk-access/templates 📦

WIP - starting point for writing Dockerfiles and CWL code from scratch

Language: Common Workflow Language - Size: 8.79 KB - Last synced: 9 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

msk-access/GetBaseCountsMultiSample Fork of zengzheng123/GetBaseCountsMultiSample

Language: C++ - Size: 2.82 MB - Last synced: 9 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

msk-access/fgbio_postprocessing

Tools for fulcrum bam processing

Language: Python - Size: 42 KB - Last synced: 9 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

msk-access/docker_multiple_tools

Containers for miscellaneous tools used by ACCESS workflows

Language: Dockerfile - Size: 5.86 KB - Last synced: 9 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

msk-access/access_utils

Miscelaneous Scripts for MSK-ACCESS workflows

Language: Python - Size: 42 KB - Last synced: 9 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

msk-access/nucleo_qc

Quality Control Workflow for UMI based BAMs

Language: Common Workflow Language - Size: 25.1 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

msk-access/sequence_qc

Noise calculations from BAM file

Language: Python - Size: 1.06 MB - Last synced: 4 days ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

msk-access/merge_fastq

Package to merge multiple pair of pair-end fastq data

Language: Python - Size: 62.5 KB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 3 - Forks: 1

msk-access/cwl_pass_through

Blank CWL for Voyager Operators that don't use cwls.

Language: Common Workflow Language - Size: 0 Bytes - Last synced: 6 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

msk-access/access_data_analysis

Scripts for downstream analysis plotting of pipeline output

Language: R - Size: 732 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 6 - Forks: 0

msk-access/nucleo

Workflow that creates all the BAM files for the cfDNA assay based FASTQ file at MSK

Language: Common Workflow Language - Size: 915 KB - Last synced: 4 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 1

msk-access/cwl_subworkflows

A list of subworkflows used for MSK-ACCESS data processing.

Language: Common Workflow Language - Size: 907 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 2 - Forks: 1

msk-access/biometrics

Python package to calculate various sample contamination metrics.

Language: Python - Size: 3.81 MB - Last synced: 4 days ago - Pushed: about 1 year ago - Stars: 3 - Forks: 1

msk-access/chip-var

Workflow for calling and annotating CHIP variants

Size: 893 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0

msk-access/access_artifacts

This repo tracts recurrent artifacts that we observe in MSK-ACCESS data

Size: 12.7 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

msk-access/cwl-commandlinetools Fork of mskcc/cwl-commandlinetools

Central location for CWL CommandLineTools

Language: Common Workflow Language - Size: 1.1 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 4 - Forks: 0

msk-access/puma_biliary_tract_summit_trial

Data for Targeting HER2 mutant advanced biliary tract cancers with neratinib: results from the SUMMIT ‘basket’ trial

Size: 16.6 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

msk-access/.github

Size: 2.02 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

msk-access/MultiQC Fork of ewels/MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

Language: Python - Size: 24.5 MB - Last synced: 9 months ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 0

msk-access/access_qc_generation

Generation Quality Controls Files for MSK-ACCESS

Language: Common Workflow Language - Size: 6.16 MB - Last synced: 4 months ago - Pushed: over 1 year ago - Stars: 1 - Forks: 1

msk-access/uncollapsed_bam_generation

Workflow for making MSK-ACCESS standard binary alignment mapping file.

Language: Common Workflow Language - Size: 1.82 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 0 - Forks: 2

msk-access/msk_lib Fork of murphycj2/msk_lib

Misc. tools that may be useful for others at MSK.

Size: 13.7 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

msk-access/python_bed_lookup Fork of MikeDacre/python_bed_lookup

Rapid lookups by coordinate from a bed file

Size: 29.3 KB - Last synced: about 1 year ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

msk-access/spectrum

Package for downstream analysis of results generated by ACCESS workflows

Language: Python - Size: 40 KB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 0 - Forks: 1

msk-access/bam_collapsing

Workflow for collapsing of standard binary alignment mapping file generated by MSK-ACCESS

Language: Common Workflow Language - Size: 1.62 MB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 0 - Forks: 1

msk-access/cookiecutter-pypackage Fork of audreyfeldroy/cookiecutter-pypackage

Cookiecutter template for a Python package.

Language: Python - Size: 513 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

msk-access/structural_variation

Language: Makefile - Size: 13.7 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

msk-access/copynumber_variation

Language: Makefile - Size: 13.7 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

msk-access/microsatellite_instability

Language: Makefile - Size: 13.7 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

msk-access/mskaccess_operators

Operators for creating input JSON using provided metadata

Language: Python - Size: 22.5 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0