Al3n70rn

ALTRE

ALTered Regulatory Elements

awesome-clonality

A curated list of awesome clonality and tumor heterogeneity resources

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

CLOSE

Cna and LOh analysis with SEquencing data

clustering_on_transcript_compatibility_counts

Clustering cells from single cell RNA seq assays

deconstructSigs

deconstructSigs

deepmedic

Efficient Multi-Scale 3D Convolutional Neural Network for Brain Lesion Segmentation

fluff

Fluff is a Python package that contains several scripts to produce pretty, publication-quality figures for next-generation sequencing experiments.

gglabeller

Shiny gadget for labeling points on ggplot

gtrellis

Genomic plot in trellis layout

Immunophenogram

ipython

Official repository for IPython itself. Other repos in the IPython organization contain things like the website, documentation builds, etc.

isovar

Abundance quantification of distinct transcript sequences containing somatic variants from cancer RNAseq

migec

A RepSeq processing swiss-knife

migmap

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

OptiType

Precision HLA typing from next-generation sequencing data

pyradiomics

Open-source python package for the extraction of Radiomics features from 2D and 3D images and binary masks.

shinyheatmap

Create user-friendly, highly customizable static and interactive biological heatmaps in a web browser

smartas

Jupyter notebook of the smartas project.

SplitThreader

Explore rearrangements and copy-number amplifications in a cancer genome

styles

Official repository for Citation Style Language (CSL) citation styles.

sv_tools

A few tools for plotting and reasoning about genomic structural variants.

tcr

tcR: an R package for immune receptor repertoire advanced data analysis.

topiary

Predict mutated T-cell epitopes from sequencing data

treeomics

Decrypting somatic mutation patterns to reveal the evolution of cancer

varcode

Library for manipulating genomic variants and predicting their effects

vdjdb-db

Git-based TCR database storage & management. Submissions welcome!

vdjtools

Post-analysis of immune repertoire sequencing data

vdjviz

A lightweight immune repertoire browser

WVPlots

Pre-packaged plots in R (on top of ggplot2)