Stars
UC Santa Cruz Computational Genomics Lab's Toil-based RNA-seq pipeline
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
A collection of video resources for machine learning
Preprocessing of single-cell RNA-Seq (deprecated)
A small library for automatical adjustment of text position in matplotlib plots to minimize overlaps.
📍 Repel overlapping text labels away from each other in your ggplot2 figures.
pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)
R package to model time series accounting for noise in the temporal dimension. Specifically designed for single cell transcriptome experiments.
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
python / numpy / pandas / patsy version of ComBat for removing batch effects.
Fast, flexible and easy to use probabilistic modelling in Python.
scLVM is a modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources, thereby allowing for the correction of confounding sources…
Reproducible machine learning analysis of gene expression and alternative splicing data
IsFinder find virus insertion site in host genomic DNA from pair end NGS data
The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.
Rapid Mapping-based Isoform Quantification from RNA-Seq Reads
GeneExpressMap makes possible the rapid, three-dimensional analysis of multiplex fluorescent whole mount in situ hybridizartion (F-WMISH) data at single cell resolution. It relies on the assignment…