Stars
A curated list of awesome Machine Learning frameworks, libraries and software.
Open source code for AlphaFold.
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Single-cell analysis in Python. Scales to >1M cells.
RNAseq analysis notes from Ming Tang
python module to plot beautiful and highly customizable genome browser tracks
Python library to facilitate genome assembly, annotation, and comparative genomics
Phylogenetic orthology inference for comparative genomics
Tools to process and analyze deep sequencing data.
Structural variation caller using third generation sequencing
Plot structural variant signals from many BAMs and CRAMs
Software package for assigning SARS-CoV-2 genome sequences to global lineages.
Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses
Plotting scripts for long read sequencing data
Sequence correction provided by ONT Research
A PyTorch Basecaller for Oxford Nanopore Reads
HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
Customizable workflows based on snakemake and python for the analysis of NGS data
Data and analysis for NA12878 genome on nanopore
GTEx & TOPMed data production and analysis pipelines
Read-based phasing of genomic variants, also called haplotype assembly
a lightweight db framework for exploring genetic variation.
A comparison of different Oxford Nanopore basecallers
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.