mital14's repositories
aws-elastic-beanstalk-express-js-sample
Sample web application for the AWS DevOps Engineer Learning Path.
BioQueue
A novel pipeline framework to accelerate bioinformatics analysis
clinvar-kaggle
Scripts used to generate the ClinVar conflicting classifications dataset on Kaggle
containers
Bioinformatics containers
DISCVRSeq
A collection of command line tools for working with sequencing data
DNAfusion
Identification of gene-fusions, including EML4-ALK
FindDNAFusion
FindDNAFusion is a combinatorial pipeline for the detecton of cancer-associated gene fusions in next-generation DNA sequencing data.
FusionInspector
FusionInspector code
IgCaller
Python program designed to reconstruct immunoglobulin gene rearrangements and oncogenic translocations from WGS, WES and capture NGS in lymphoid neoplasms.
InterVar
A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline
JuLI
Junction Location Identifier (JuLI): DNA fusion detection tool for clinical sequencing.
jvarkit
Java utilities for Bioinformatics
learning
BioInformatics
msisensor-pro
Microsatellite Instability (MSI) detection using high-throughput sequencing data.
MutationalPatterns
R package for extracting and visualizing mutational patterns in base substitution catalogues
ncov
Nextstrain build for novel coronavirus SARS-CoV-2
NIPT_Informatics
Non-Invasive Prenatal Testing (NIPT) size selection and deduplication pipeline
Reverse_Complement
Bioinformatics one-liner to reverse complement the DNA Sequence
rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
SigProfilerExtractor
SigProfilerExtractor
SigProfilerMatrixGenerator
SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.
STAR-Fusion
STAR-Fusion codebase
TCGAmutations
R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)
tre
The approximate regex matching library and agrep command line tool.
vcfstats
Powerful statistics for VCF files
vg
tools for working with genome variation graphs
WisecondorX
WisecondorX — An evolved WISECONDOR