Valentine Svensson

ctra. Complex trait regulatory architectures

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

ormachine. Python

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

ml-videos. A collection of video resources for machine learning

svae. code for Structured Variational Autoencoders

scRNA-Seq-TCC-prep. Preprocessing of single-cell RNA-Seq (deprecated)

GPflow. Gaussian processes in TensorFlow

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

ggrepel. :round_pushpin: Repel overlapping text labels away from each other in your ggplot2 figures.

patsylearn. Patsy Adaptors for Scikit-learn

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

cyclone. cyclone

kallisto. Near-optimal RNA-Seq quantification

embeddr. This repository is retired software

curver. Curve reconstruction from noisy points

GPy. Gaussian processes framework in python

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

deML. Maximum likelihood demultiplexing

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

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

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

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.

monocle-release. R

flotilla. Reproducible machine learning analysis of gene expression and alternative splicing data

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

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

sailfish. Rapid Mapping-based Isoform Quantification from RNA-Seq Reads

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.

MIMOSA. Mixture Models for Single Cell Assays

MAST. Tools and methods for analysis of single cell assay data in R

sphinxtr. The Sphinx Thesis Resource

algorithms. This repository is not maintained

importing_issue. Python

analytical-tutorials. Tutorials for writing analytical scripts

Boutonniere. Python

scilifelab_bcbio. Scilifelab-specific code for bcbio-nextgen, linked via git submodules

scilifelab. Misc code snippets for Science For Life Laboratory

modules.sf.net. Adhoc software "packaged" for the ancient and deprecated "module system" (http://modules.sf.net/)

status. Tornado web app for visualizing information and statistics regarding SciLifeLab Genomics platform operations.

DD3003. Parallel Computing: Theory - Hardware - Software with Special Focus on Multi-Core Programming

scilifelab. Misc code snippets for Science For Life Laboratory

modules.sf.net. Adhoc software "packaged" for the ancient and deprecated "module system" (http://modules.sf.net/)

rickshaw. JavaScript toolkit for creating interactive real-time graphs

sublime-text-git. Plugin for some git integration into sublime text

battleship-bot. Experimentation with battledhip strategies

scilife-utilities. Helper scripts for NGS data processing

bcbb. Useful bioinformatics code, primarily in Python and R

scikits.image. Image Processing SciKit (Toolbox for SciPy)

remix. Echo Nest Remix: The Internet Synthesizer

matplotlib. Python

matplotlib. matplotlib: plotting with Python

inscight. inSCIght: The Scientific Computing Podcast

Scribl. HTML5 canvas genomic graphics library

d3. Bring data to life with SVG, Canvas and HTML. :bar_chart::chart_with_upwards_trend::tada:

bcbb. Useful bioinformatics code, primarily in Python and R

scikits.image. This repository now lives at https://github.com/scikit-image/scikit-image

bcbb. Incubator for useful bioinformatics code, primarily in Python and R