Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
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Updated
Jun 22, 2024 - Python
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Intervene: a tool for intersection and visualization of multiple genomic region and gene sets
Earl Grey: A fully automated TE curation and annotation pipeline
H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)
Long-reads Gap-free Chromosome-scale Assembler
A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
non-redundant, compressed, journalled, file-based storage for biological sequences
Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)
Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s)
provides common tools and lookup tables used primarily by the hgvs and uta packages
A python project for analysis of codon usage for gene or genome analysis
A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes
NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data
Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data
[in development] Proof-of-Concept variation translation, validation, and registration service
Viral genome assemble and characterisation
Archived code for analyses in "Extensive phylogenomic discordance and the complex evolutionary history of the Neotropical cat genus Leopardus" (Lescroart et al. 2023, MBE)
Computational programs and algorithms used to convert information from biochemical experiments (DNA/RNA/Protein/DNA chip/NGS) into useful information and data.
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