Ambarish Kumar's repositories
2018-11-29-Crick-London
Version of Data Carpentry in R Course for CRUK FCI,London
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
broad-prod-wgs-germline-snps-indels
Workflows used in production at Broad for germline short variant discovery in WGS data
cephis
Evolution of the `ches` repository to include all support libraries and PDFBox2
ChemIdConvert
Chemical identifier conversion REST Api
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-data-processing
Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
gatk4-germline-snps-indels
Workflows for germline short variant discovery with GATK4
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
getpapers
Get metadata, fulltexts or fulltext URLs of papers matching a search query
intel-gatk4-germline-snps-indels
Workflows for germline short variant discovery with GATK4 optimized by Intel for on-premises infrastructure
neat-genreads
NEAT read simulation tools
normami-1
A tool to convert a variety of inputs into normalized, tagged, XHTML (with embedded/linked SVG and PNG where appropriate).
nycflights13
An R data package containing all out-bound flights from NYC in 2013 + useful metdata
OpenScienceCitizenInitiative
Project to set up, organize, and govern an EU Citizen Initiative about Open Science
pubmedWikidata
Small project to get information about PubMed articles from Wikidata.
R4R
This Repository contains the complete course material for the First TIGR2ESS FP2/FP3 Workshop on R for Genomics and Data Mining.
RNAseq_September_2018
Introduction to RNAseq Data Analysis - September 2018
RSEM
RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
SV2
Support Vector Structural Variation Genotyper
taxonlookup
A versioned and dynamically updating taxonomic lookup table for land plants
tigr2ess
Materials for TIGR2ESS workshop in Delhi Feb 2019 - joint UK(Cambridge) - India project on Food Security.
trinityrnaseq
Trinity RNA-Seq de novo transcriptome assembly
ViTA
Predict genomic variants encoded HLA-epitopes