csgroen

scycle

Cell cycle pseudotime in single-cell RNA-seq

RTN_example_TCGA_LIHC

Example of data preprocessing for RTNsurvival, using the TCGA-LIHC cohort

freshinstall

UFPR Bioinformatics Lab fresh install bash script

ggheatmapper

Tile-able heatmaps using ggheatmap and patchwork

classifyT1BC

Classification of T1 Bladder Cancer

deconverse

Bulk RNA-seq deconvolution and benchmarking using single-cell reference profiles

RTNsurvival

RTNsurvival: An R/Bioconductor package for survival analysis using transcriptional networks and regulons

abbreviations

blog_example

Minimal reproducible analysis example

cit_blca_proteomics

Reproducible code for all analyses in bladder cancer proteomics manuscript

consensusMIBCweb

Temporary: A webapp version of the consensusMIBC R package

csgroen.github.io

Blog

deconverse_data

Data cache for deconverse

dotfiles

some of my dotfiles

ecotyper

elpigraph-python

Python implementation of the ElPiGraph algorithm with cpu and gpu support

ggplot2

An implementation of the Grammar of Graphics in R

hyde

A brazen two-column theme for Jekyll.

infercnvpy

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

mibcCPIclass

mkdocs

Project documentation with Markdown.

NCBI_Taxonomy_Search

Search locally hosted NCBI Taxonomy using Flask

Rbasics

RTNduals

Regulatory loops using networks inferred by RTN.

salmon

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

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

scycle_notebooks

sphinx_rtd_theme

Sphinx theme for readthedocs.org

Stabilized_ICA

This repository proposes a python implementation of a stabilized ICA algorithm

styles

Official repository for Citation Style Language (CSL) citation styles.