rptashkin

beagle

Voyager Backend

beyonce

:crown: :bee: :bar_chart: Beyoncé colour palettes for R

covfefe

Color palettes that will have covfefe of 45's blunders

cumc_risk_calculator

Shiny application to calculate risk score from model params

facets2n

Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations

msisensor

microsatellite instability detection using tumor only or paired tumor-normal data

oncoPrintr

R package to generate onco prints of genomic and clinical data of patient cohorts

TCGA_miRNASeq_matrix

miRNAseq data matrix from downloaded TCGA data

vcf2maf

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

rptashkin/TCGA_miRNASeq_matrix

miRNAseq data matrix from downloaded TCGA data

rptashkin/facets2n

Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations

rptashkin/covfefe

Color palettes that will have covfefe of 45's blunders

rptashkin/beyonce

:crown: :bee: :bar_chart: Beyoncé colour palettes for R

rptashkin/beagle

Voyager Backend

rptashkin/cumc_risk_calculator

Shiny application to calculate risk score from model params

rptashkin/msisensor

microsatellite instability detection using tumor only or paired tumor-normal data

rptashkin/vcf2maf

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

rptashkin/biometrics

Python package to calculate various sample contamination metrics.

rptashkin/CODECsuite

analysis pipeline for CODEC data

rptashkin/Conpair

Concordance and contamination estimator for tumor-normal pairs

rptashkin/couplet

rptashkin/facets

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.

rptashkin/facets-preview

Load, review and adjust facets fits

rptashkin/facets-suite

Tools for copy-number analysis using FACETS

rptashkin/igv-reports

Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.

rptashkin/IGV-snapshot-automator

Script to automatically create and run IGV snapshot batchscripts

rptashkin/impact-annotator_v2

Develop a knowledge-based approach using MSK-IMPACT data to build an automatic variant classifier

rptashkin/ipssm

Molecular International Prognostic Scoring System IPSS-M for Myelodysplastic Syndromes

rptashkin/joblib

Computing with Python functions.

rptashkin/maftools

Summarize, Analyze and Visualize MAF files from TCGA or in house studies.

rptashkin/mergeSVvcf

Python package and routines for merging SV VCF files

rptashkin/parabricks-omics-private-workflows

For running private Parabricks workflows on Amazon Omics

rptashkin/pctGCdata

R datasets of GC percentages for human and mouse genomes

rptashkin/PureCN

Copy number calling and variant classification using targeted short read sequencing

rptashkin/ridgeback

Toil API

rptashkin/Sarek

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

rptashkin/SigProfilerSingleSample

SigProfilerSingleSample allows attributing a known set of mutational signatures to an individual sample. The tool identifies the activity of each signature in the sample and assigns the probability for each signature to cause a specific mutation type in the sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

rptashkin/textplot

rptashkin/toil_cnacs

toil wrapper for CNACS