jhu99

scbean

Single-cell data analysis

miteFinder

vipcca

Single-cell alignment

NetCoffee2

scanalyse

C++ library for single cell analyses

BiwalkLDA

davae_paper

db_hand

Connector of NCBI databases

GRNLMM

gene regulatory network with linear mixed model

twadn

Time wrapping algorithm for aligning dynamic networks

Batch-effect-removal-benchmarking

A benchmark of batch-effect correction methods for single-cell RNA sequencing data

dca

Deep count autoencoder for denoising scRNA-seq data

dec

desc

Deep Embedding for Single-cell Clustering

ExpansionHunter

A tool for estimating repeat sizes

GCNPCC

gene co-expression networks using partial correlation coefficients

jhulab

a template for research group sites

ScaleHD

Automated DNA micro-satellite genotyping

scanpy

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

scRNA.seq.datasets

Collection of public scRNA-Seq datasets used by our group

scvae

Deep learning for single-cell transcript counts

seqan

SeqAn's official repository.

seqan3

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

seurat-wrappers

Community-provided extensions to Seurat

SPARK

Spatially resolved transcriptomic analysis

SPARK-Analysis

spatially resolved data analysis

st_pipeline

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

VIMCCA_paper

vipcca_paper