vals's Stars
jmschrei/pomegranate
Fast, flexible and easy to use probabilistic modelling in Python.
seandavi/awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
SheffieldML/GPy
Gaussian processes framework in python
GPflow/GPflow
Gaussian processes in TensorFlow
dustinvtran/ml-videos
A collection of video resources for machine learning
Phlya/adjustText
A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps.
slowkow/ggrepel
:round_pushpin: Repel overlapping text labels away from each other in your ggplot2 figures.
COMBINE-lab/salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
pachterlab/kallisto
Near-optimal RNA-Seq quantification
mattjj/svae
code for Structured Variational Autoencoders
cole-trapnell-lab/monocle-release
TGAC/KAT
The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.
kingsfordgroup/sailfish
Rapid Mapping-based Isoform Quantification from RNA-Seq Reads
YeoLab/flotilla
Reproducible machine learning analysis of gene expression and alternative splicing data
PMBio/scLVM
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 of variation.
brentp/combat.py
python / numpy / pandas / patsy version of ComBat for removing batch effects.
pachterlab/scRNA-Seq-TCC-prep
Preprocessing of single-cell RNA-Seq (deprecated)
brentp/hts-python
pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)
amueller/patsylearn
Patsy Adaptors for Scikit-learn
grenaud/deML
Maximum likelihood demultiplexing
BD2KGenomics/toil-rnaseq
UC Santa Cruz Computational Genomics Lab's Toil-based RNA-seq pipeline
PMBio/cyclone
cyclone
JohnReid/DeLorean
R package to model time series accounting for noise in the temporal dimension. Specifically designed for single cell transcriptome experiments.
kieranrcampbell/embeddr
This repository is retired software
RGLab/MIMOSA
Mixture Models for Single Cell Assays
TammoR/ormachine
a-slide/IsFinder
IsFinder find virus insertion site in host genomic DNA from pair end NGS data
aksarkar/ctra
Complex trait regulatory architectures
coreyflynn/GeneExpressMap
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 of F-WMISH signal to individual cells based on the proximity of cytoplasmic hybridization signal to cell nuclei. GeneExpress3D greatly extends the power of multiplex F-WMISH for analyzing patterns of gene expression and is a powerful tool for gene regulatory network analysis.
kieranrcampbell/curver
Curve reconstruction from noisy points