Pinned Repositories
7z
Because 7-zip source code was in a 7z archive [mirror]
AAF
alignment and assembly free
abutils
Models, functions and visualization tools for working with adaptive immune receptore repertoire (AIRR) data.
alphafold
Open source code for AlphaFold.
genomeassembly
Implementation of ToL genome assembly workflows
hisat2
Graph-based alignment (Hierarchical Graph FM index)
MetaTiME
MetaTiME: Meta-components in Tumor immune MicroEnvironment
RoseTTAFold2
samtools
Tools (written in C using htslib) for manipulating next-generation sequencing data
USalign
Universal Structure Alignment of Monomeric and Complex Structure of Nucleic Acids and Proteins
wook2014's Repositories
wook2014/BioSAK
A Swiss-Army-Knife for Bioinformaticians
wook2014/CeleScope
Single Cell Analysis Pipelines
wook2014/COMPASS
COpy number and Mutations Phylogeny from Amplicon Single-cell Sequencing This tool can be used to infer a tree of somatic events (mutations and copy number alterations) that occurred in a tumor.
wook2014/deepredeff
predict effector protein
wook2014/dictys
Context specific and dynamic gene regulatory network reconstruction and analysis
wook2014/fasta36
Git repository for FASTA36 sequence comparison software
wook2014/fastcat
Simple utility to concatenate .fastq(.gz) files whilst creating a summary of the sequences.
wook2014/flair
Full-Length Alternative Isoform analysis of RNA
wook2014/Flame
Flame: A web tool for functional enrichment analysis using multiple gene lists
wook2014/ggCaller
Bifrost graph gene caller.
wook2014/GSEApy
Gene Set Enrichment Analysis in Python
wook2014/IsoQuant
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
wook2014/Jovian_archive
Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical biologists and wet-lab personnel to do metagenomics/viromics analyses themselves, without bioinformatics expertise.
wook2014/kallisto
Near-optimal RNA-Seq quantification
wook2014/lifelines
Survival analysis in Python
wook2014/MIDAS2
Metagenomic Intra-Species Diversity Analysis 2
wook2014/Monopogen
SNV calling from single cell sequencing
wook2014/PACT
A pipeline for analysis of circulating tumor DNA
wook2014/phast
PHAST: PHYLOGENETIC ANALYSIS WITH SPACE/TIME MODELS
wook2014/phyml
PhyML -- Phylogenetic estimation using (Maximum) Likelihood
wook2014/repaq
A fast lossless FASTQ compressor with ultra-high compression ratio
wook2014/RINmaker
wook2014/rmats-turbo
MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold
wook2014/RoseTTAFold
This package contains deep learning models and related scripts for RoseTTAFold
wook2014/ruffus
CGAT-ruffus is a lightweight python module for running computational pipelines
wook2014/sinto
Tools for single-cell data processing
wook2014/SQANTI3
Tool for the Quality Control of Long-Read Defined Transcriptomes
wook2014/TALON
Technology agnostic long read analysis pipeline for transcriptomes
wook2014/trackplot
trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets.
wook2014/unialigner
UniAligner (formerly, TandemAligner) is the first parameter-free algorithm for sequence alignment that introduces a sequence-dependent alignment scoring that automatically changes for any pair of compared sequences