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/RoseTTAFold2
wook2014/ANIclustermap
A tool for drawing ANI clustermap between all-vs-all microbial genomes
wook2014/bioconda-utils
Utilities for building and managing bioconda recipes
wook2014/BioSeqUtils
Extract Sequence from Genome According to Annotation File
wook2014/cobs
COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)
wook2014/deepgoplus
DeepGO with GOPlus axioms
wook2014/EsViritu
Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
wook2014/foldcomp
Compressing protein structures effectively with torsion angles
wook2014/gatb-core
Core library of the Genome Analysis Toolbox with de-Bruijn graph
wook2014/ggally
R package that extends ggplot2
wook2014/ggkegg
Analyzing and visualizing KEGG information using the grammar of graphics
wook2014/kraken2
The second version of the Kraken taxonomic sequence classification system
wook2014/MetaMaps
Long-read metagenomic analysis
wook2014/METAMVGL
METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs
wook2014/MUFFIN
hybrid assembly and differential binning workflow for metagenomics, transcriptomics and pathway analysis
wook2014/nglview
Jupyter widget to interactively view molecular structures and trajectories
wook2014/orthologr
Genome wide orthology inference and dNdS estimation
wook2014/PANDA-3D
Protein function prediction based on alphaFold models
wook2014/PANDA2
PANDA2, which used the cutting-edge graph neural network to model the GO DAG
wook2014/protein_analysis_tools
USAlign, Rosetta, Amber and other apps script analysis
wook2014/psix
a computational tool for identifying cell-state associated alternative splicing events in scRNA-seq data
wook2014/RFdiffusion
Code for running RFdiffusion
wook2014/singleCellTK
Interactively analyze single cell genomic data
wook2014/SUPPA
SUPPA: Fast quantification of splicing and differential splicing
wook2014/Surfaces
Surfaces, an easy to use, fast and customizable software for quantification and visualization of molecular interactions based on the calculation of surface areas in contact. Surfaces calculations shows equivalent or better correlations with experimental data as computationally expensive methods based on molecular dynamics.
wook2014/taxoniq
Taxon Information Query - fast, offline querying of NCBI Taxonomy and related data
wook2014/TCGAplot
A number of functions were generated to perform pan-cancer DEG analysis, correlation analysis between gene expression and TMB, MSI, TIME, and promoter methylation. Methods for visualization were provided in order to easily perform integrative pan-cancer multi-omics analysis.
wook2014/ViennaRNA
A C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures
wook2014/wf-transcriptomes
This workflow identifies RNA isoforms using either cDNA or direct RNA (dRNA) Oxford Nanopore reads.
wook2014/zol
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)