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batch-effect-removal-benchmarking

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

biwalklda

davae_paper

db_hand

Connector of NCBI databases

dca

Deep count autoencoder for denoising scRNA-seq data

dcn-new

Updated version of DCN

dec

desc

Deep Embedding for Single-cell Clustering

expansionhunter

A tool for estimating repeat sizes

gcnpcc

gene co-expression networks using partial correlation coefficients

grnlmm

gene regulatory network with linear mixed model

jhulab

a template for research group sites

localali

Automatically exported from code.google.com/p/localali

mitefinder

netcoffee

Automatically exported from code.google.com/p/netcoffee

netcoffee2

r_package_mitefinder

scalehd

Automated DNA micro-satellite genotyping

scanalyse

C++ library for single cell analyses

scanpy

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

scbean

Single-cell data analysis

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