Ambarish Kumar's repositories
neat-genreads
NEAT read simulation tools
pubmedWikidata
Small project to get information about PubMed articles from Wikidata.
broad-prod-wgs-germline-snps-indels
Workflows used in production at Broad for germline short variant discovery in WGS data
tigr2ess
Materials for TIGR2ESS workshop in Delhi Feb 2019 - joint UK(Cambridge) - India project on Food Security.
dictionaries
Dictionaries for use with `ami` , including some management software
gatk4-cnn-variant-filter
This repo provides workflows that takes advantage of GATKs CNN tool
gatk4-germline-snps-indels
Workflows for germline short variant discovery with GATK4
gatk4-data-processing
Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
trinityrnaseq
Trinity RNA-Seq de novo transcriptome assembly
taxonlookup
A versioned and dynamically updating taxonomic lookup table for land plants
gatk4-mitochondria-pipeline
Workflow for SNP and INDEL variant calling on mitochondria.
generic-wdl-script
This generic wdl script will be for users seeking to quickly run a shell command
R4R
This Repository contains the complete course material for the First TIGR2ESS FP2/FP3 Workshop on R for Genomics and Data Mining.
ami-jars
point releases of ami executables (normally as maven-appassembler jar-with-dependencies)
nycflights13
An R data package containing all out-bound flights from NYC in 2013 + useful metdata
2019-01-15-CRUK-Cambridge-DCinR
Data Carpentry in R course held at School of Clinical Medicine, Cambridge
arcsv
Complex structural variant detection from WGS data
normami
Merger of Norma and Ami
2018-11-29-Crick-London
Version of Data Carpentry in R Course for CRUK FCI,London
ChemIdConvert
Chemical identifier conversion REST Api
ViTA
Predict genomic variants encoded HLA-epitopes
RSEM
RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
RNAseq_September_2018
Introduction to RNAseq Data Analysis - September 2018
getpapers
Get metadata, fulltexts or fulltext URLs of papers matching a search query
normami-1
A tool to convert a variety of inputs into normalized, tagged, XHTML (with embedded/linked SVG and PNG where appropriate).
cephis
Evolution of the `ches` repository to include all support libraries and PDFBox2
OpenScienceCitizenInitiative
Project to set up, organize, and govern an EU Citizen Initiative about Open Science
intel-gatk4-germline-snps-indels
Workflows for germline short variant discovery with GATK4 optimized by Intel for on-premises infrastructure
SV2
Support Vector Structural Variation Genotyper