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Complex trait regulatory architectures

Python 1 Updated Nov 11, 2017

UC Santa Cruz Computational Genomics Lab's Toil-based RNA-seq pipeline

Python 40 10 Updated Aug 17, 2020
Python 5 2 Updated May 1, 2018

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

3,279 998 Updated Dec 4, 2024

A collection of video resources for machine learning

1,537 213 Updated Jan 23, 2021

code for Structured Variational Autoencoders

Python 351 87 Updated Aug 22, 2018

Preprocessing of single-cell RNA-Seq (deprecated)

Jupyter Notebook 62 26 Updated Jul 5, 2019

Gaussian processes in TensorFlow

Python 1,858 434 Updated Jan 21, 2025

A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps.

Jupyter Notebook 1,522 88 Updated Oct 31, 2024

📍 Repel overlapping text labels away from each other in your ggplot2 figures.

R 1,228 96 Updated Nov 4, 2024

Patsy Adaptors for Scikit-learn

Python 48 12 Updated Apr 17, 2019

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

Python 49 18 Updated Mar 3, 2017

cyclone

HTML 18 12 Updated Jul 21, 2015

Near-optimal RNA-Seq quantification

C 671 173 Updated Dec 3, 2024

This repository is retired software

R 12 3 Updated Oct 29, 2015

Curve reconstruction from noisy points

R 1 Updated Mar 18, 2015

Gaussian processes framework in python

Python 2,064 566 Updated Jan 15, 2025

R package to model time series accounting for noise in the temporal dimension. Specifically designed for single cell transcriptome experiments.

TeX 15 4 Updated Sep 24, 2021

Maximum likelihood demultiplexing

C++ 46 14 Updated Feb 9, 2023

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

C++ 784 164 Updated May 29, 2024

python / numpy / pandas / patsy version of ComBat for removing batch effects.

Python 103 44 Updated Dec 31, 2018

Fast, flexible and easy to use probabilistic modelling in Python.

Python 3,400 588 Updated Jan 8, 2025

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…

HTML 104 46 Updated Dec 16, 2022

Reproducible machine learning analysis of gene expression and alternative splicing data

Jupyter Notebook 127 25 Updated Apr 15, 2023

IsFinder find virus insertion site in host genomic DNA from pair end NGS data

Python 1 1 Updated Jul 31, 2014

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.

C++ 211 52 Updated Nov 25, 2022

Rapid Mapping-based Isoform Quantification from RNA-Seq Reads

C++ 126 45 Updated Jun 9, 2022

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…

Objective-C 1 Updated Jun 21, 2011

Mixture Models for Single Cell Assays

R 7 2 Updated Jun 1, 2021
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