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ngs_pipeline

Exome/Capture/RNASeq Pipeline Implementation using snakemake

pvac-seq

A cancer immunotherapy pipeline

py.bio

radmixture

an R package for ancestry analysis

reseqtools

A Toolkit for analyzing next-generation DNA Re-Sequencing data

rna-seq-analysis

RNAseq analysis notes from Tommy Tang

rna-seq-diff-exprn

RNA-Sequencing data differential expression analysis pipeline. Performs: genome coverage (via bedtools and HTSeq), generates Circos code and plots, differential expression (via DESeq and NOISeq), structural variant detection (e.g. fusion genes, via SVDetect) and differential exon usage (via DEXSeq).

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

rtcr

A pipeline for complete and accurate recovery of TCR repertoires from high throughput sequencing data.

sctcrseq

Processing of single cell RNAseq data for the recovery of TCRs in python

snakefiles

:snake: Snakefiles for common RNA-seq data analysis workflows.

startrac

STARTRAC(Single T-cell Analysis by Rna-seq and Tcr TRACking)

tcr

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

tcr-1

Web-application for T cell receptors' repertoires analyzing

tcr-2

A pipe for extracting TCRs from RNAseq data.

tcr-3

:exclamation: This is a read-only mirror of the CRAN R package repository. tcR — Advanced Data Analysis of Immune Receptor Repertoires. Homepage: http://imminfo.github.io/tcr/ Report bugs for this package: https://github.com/imminfo/tcr/issues

tcr-analysis

Scripts and files that I use to analyse T cell receptor repertoire data, produced by deep-sequencing

tcr-dist

Software tools for the analysis of epitope-specific T cell receptor (TCR) repertoires (scroll down for the README)

tcr-from-rnaseq2015

Code associated with Brown, Raeburn, and Holt, Profiling tissue-resident T cell repertoires by RNA sequencing, Genome Medicine 2015

tcrclust

A collection of scripts used for tracking T-cell expansions using HTS

umi-analysis

Scripts for processing Illumina sequence data containing unique molecular identifiers (UMI)

umitools

Tools to handle reads sequenced with unique molecular identifiers (UMIs).

varscan

Cloned from https://sourceforge.net/projects/varscan, with possible improvement