JakeConway

ClinPlots

R package to create clinico-genomic charts

JakeConway.github.io

upset

UpSet - Visualizing Intersecting Sets

fastQCvis

New visualizations for fastQC files

3dbarplot

A 3D barplot script for R. Can encode variables using both height and depth of columns.

biostats_r_code

Repo for R code for my class

cs181-demos

IPython demos for CS181

deconstructSigs

deconstructSigs

expands

Expanding Ploidy and Allele Frequency on Nested Subpopulations (expands) characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data.

FoundationToFHIR

FoundationToFHIRjs

FoundationToFHIRpy

hif2gene

mstknnclust

:exclamation: This is a read-only mirror of the CRAN R package repository. mstknnclust — MST-kNN Clustering Algorithm

PCM-survival

SigProfilerExtractor

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

somalier

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs

TensorFlow-Tutorials

TensorFlow Tutorials with YouTube Videos