lybird300

2017_2018-single-cell-RNA-sequencing-Workshop-UCD_UCB_UCSF

2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF

calculate_mutational_burden

A lightweight python script to calculate mutational burden.

cancer

cancer-genomics-workflow

MGI's CWL Cancer Pipelines.

chimeraviz

chimeraviz is an R package that automates the creation of chimeric RNA visualizations.

CLCA_WGS

Deep whole-genome analysis of 494 hepatocellular carcinomas

CMG

Pipeline development for NGS analysis

CNTools

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/CNTools.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=CNTools.

CovGen

Creates a target specific exome_full192.coverage.txt file required by MutSig

CPTAC3-RNA-related-pipeline

Gene/transcript expression; Fusion; de novo assembly

CPTAC3.catalog

Details about CPTAC3 data at GDC and in Ding Lab

FusionVizR

gencode_regions

Extract 3'UTR, 5'UTR, CDS, Promoter, Genes from Gencode files

getting-started-with-genomics-tools-and-resources

Unix, R and python tools for genomics

immunology-informatics

Immunology Informatics - Big Data Analysis in Immunology - Tutorials

learning_bam_file

Learning the Sequence Alignment/Map format

lybird300.github.io

maftools

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

MMR

C. elegans and ICGC cancer data analysis for (Meier, Volkova et al. 2017)[https://www.biorxiv.org/content/biorxiv/early/2017/06/13/149153.full.pdf].

mutation-signatures

Create mutation signatures from MAF's, and decompose them into Stratton signatures

PanCanAtlasGermline

RNASeq2017

Course on Best Practices on RNA-Seq data analysis at the University of Salerno - 27-29 September 2017

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.

scell_lung_adenocarcinoma

This is the repository that contains the analysis of the lung adenocarcinoma single cell dataset

SomaticAmplicon

NGS pipeline for somatic variant calling from amplicon datasets

SynthEx

TranscriptomeTools

collection of transcriptome analysis software

UMI-tools

Tools for handling Unique Molecular Identifiers in NGS data sets

vg

tools for working with genome variation graphs

WEScall

WEScall: WES genotype calling pipeline