seqlib

Sequence manipulation toolkit for FASTA/FASTQ files written in Nim.

A Python script that converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. CIGAR string of SAM format is used to compute the end coordinate.

The Chromosome Ontology is an automatically derived ontology of chromosomes and chromosome parts.

Low- and high-level wrappers for Gemma's RESTful API. They enable access to curated expression and differential expression data from over 10,000 published studies. Gemma is a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles.

ScVI is a variational inference model for single-cell RNA-seq data that can learn an underlying latent space, integrate technical batches and impute dropouts. The learned low-dimensional latent representation of the data can be used for visualization and clustering.