biogeeker's repositories
atac-seq-pipeline
ENCODE ATAC-seq pipeline
vcf2phylip
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
ColabFold
Making Protein folding accessible to all via Google Colab!
reg-gen
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
MashMap
A fast approximate aligner for long DNA sequences
alphafold
Open source code for AlphaFold.
RoseTTAFold
This package contains deep learning models and related scripts for RoseTTAFold
TIRmite
Map TIR-pHMM models to genomic sequences for annotation of MITES and complete DNA-Transposons.
ATAC-seq
Basic workflow for ATAC-seq analysis
cath-tools
Protein structure comparison tools such as SSAP and SNAP
ContigsMerger
Script to merge contigs generated using different de novo assembly methods
wgap
Whole Genome Annotation Pipeline
teloclip
A tool for the recovery of unassembled telomeres from soft-clipped read alignments.
compGWAS
A python toolkit for comprehensive GWAS analysis of SNPs/Indels.
bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
wgdi-doc
ceshi
masif
MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.
dl2bioinformatics
Deep learning with bioinformatics
bedtools2
bedtools - the swiss army knife for genome arithmetic
RASP
RASP 4
snippy
:scissors: :zap: Rapid haploid variant calling and core genome alignment
Bioinformatics-with-Python-Cookbook-Second-Edition
Bioinformatics with Python Cookbook Second Edition, published by Packt
biocode
Bioinformatics code libraries and scripts
Tkinter-GUI-Application-Development-Blueprints-Second-Edition
Tkinter GUI Application Development Blueprints Second Edition, published by Packt
getting-started-with-genomics-tools-and-resources
Unix, R and python tools for genomics and data science
tutorials-1
Various tutorials about MD setup and analysis, protein-ligand docking, machine learning and lots of other interesting things.
neurips19-graph-protein-design
Generative Models for Graph-Based Protein Design