Segun Christopher Jung's repositories
CNVWorkflow_Code
CNV analysis workflow code for the manuscript
DeltaMSI
DeltaMSI: AI-based screening for microsatellite instability in solid tumors
downsampling
Downsample fastq files in an automated way
downsampling-FASTQ
FASTQ downsampling using seqtk
fastahack
utilities for indexing and sequence extraction from FASTA files
fastq-multx
Demultiplexes a fastq.
fusioncatcher
Finder of Somatic Fusion Genes in RNA-seq data
gene-outlier-detection
A Bayesian model for identifying gene expression outliers for individual single samples (N-of-1) when compared to a cohort of background datasets.
GWA_tutorial
A comprehensive tutorial about GWAS and PRS
igv
Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
jvarkit
Java utilities for Bioinformatics
mimsi
Microsatellite Instability Classification using Multiple Instance Learning
MSIFinder
MSI detect
msisensor-pro
Microsatellite Instability (MSI) detection using high-throughput sequencing data.
ngsutils
Tools for next-generation sequencing analysis
pTrimmer
Used to trim off the primer sequence from mutiplex amplicon sequencing
PureCN
Copy number calling and variant classification using targeted short read sequencing
PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
SRSLYumi
Process unique molecule identifiers (UMI) for SRSLY DNA NGS libraries
strelka
Strelka2 germline and somatic small variant caller
TMB
Tumor Mutational Burden
vcf_stuff
đź“ŠEvaluating, filtering, comparing, and visualising VCF
vcfstats
Powerful statistics for VCF files
VisualMSI
Detect and visualize microsatellite instability(MSI) from NGS data