Stars
Scripts and workflows for use analyzing UK Biobank data from the DNANexus Research Analysis Platform
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
Algorithm For Gene Order Reconstruction in Ancestors
🧬 gget enables efficient querying of genomic reference databases
milescsmith / Azimuth
Forked from jjc2718/AzimuthFork of Azimuth (Machine Learning-Based Predictive Modelling of CRISPR/Cas9 guide efficiency), updated to work with Python 3.10+
sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale
GeneWalk identifies relevant gene functions for a biological context using network representation learning
Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
Maps loop loci from ChIA-pet/Hi-C/etc. experiments across samples, which may be different species and/or cell types. Uses the bnMapper algorithm for cross-species mappings.
Python reimplementation of hicrep with compatibility for sparse matrices
Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
StrVCTVRE, a structural variant classifier for exonic deletions and duplications
Python bindings to and Jupyter Notebook+Lab integration for the HiGlass viewer
python module to plot beautiful and highly customizable genome browser tracks
PhyloAcc a software to detect the changes of conservation of a genomic region
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Tools for manipulating biological data, particularly multiple sequence alignments
Recipes for using Python's pandas library
Efficient pythonic random access to fasta subsequences