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ascend

Analysis of Single Cell Expression, Normalization and Differential expression

bbmap

(Not Offical) BBMap short read aligner, and other bioinformatic tools.

braindeconbenchmark

This study benchamrked the performance of existing cell deconvolution methods with human brain transcriptome and evaluated the biological applications of deconvoluted data in eQTL mapping and differential expression analysis.

brca_cell_atlas

Data processing and analysis related code associated with the study "A single-cell and spatially resolved atlas of human breast cancers".

cellhint

A tool for semi-automatic cell type harmonization and integration

cortexcelldeconv

deconv_benchmark

deconv_matching_bulk_scnrna

Repository for "Effective methods for bulk RNA-seq deconvolution using scRNA-seq and snRNA-seq derived transcriptomes"

decot

dwls

Gene expression deconvolution using dampened weighted least squares

gsdensity

gsdensity_manuscript_code

libra

neuroblastoma_gene_signature

Validate a gene signature for evaluating the survival of patients with neuroblastoma.

paste_reproducibility

picalo

eQTL interaction optimization using expectation maximization

rads

recount3_networks

Scripts required to replicate the analysis in - "Aggregation of publicly available RNA-seq experiments improves inference of consensus and tissue-specific Gene Co-expression Networks"

recover-counts

Recover transcript counts from log-normalized UMI counts data.

rosmap_mediation_paper

sc-shc

Significance analysis for clustering single-cell RNA-sequencing data

sc-type

seacells

SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data

spatial_scog_workshop_2022

Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022

spatialhallmarks_paper

strategies-for-cellular-deconvolution-in-human-brain-rna-sequencing-data

vsn-pipelines

A repository of pipelines for single-cell data in Nextflow DSL2

zipper_plot

Zipper plot: visualizing transcriptional activity of genomic regions