zji90

TSCAN

TSCAN: Tools for Single-Cell ANalysis

SCRAT

SCRAT: Single-Cell Regulome Analysis Tool

SCATE

SCATE: Single-cell ATAC-seq Signal Extraction and Enhancement

GEOsearch

awesome-single-cell

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

STIP

STIP: State Transition Inference Prediction

ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

ComplexHeatmap

Make Complex Heatmaps

copykat

DL_code

esvd

eSVD_evaluation

Giotto_site

Website for the Giotto spatial toolbox

HiTC

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/HiTC.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=HiTC.

ideas

Individual level Differential Expression Analysis for Single cells

jhu-dissertation-mwe

JHU Dissertation LaTeX mwe

mbImpute

mbImpute: an accurate and robust imputation method for microbiome data

MetaboAnalystR

R package for MetaboAnalyst

microbiome_taxacontrol

Code to reproduce results in the microbiome taxonomic abundances control paper

monocle3

nnSVG

nnSVG: scalable method to identify spatially variable genes (SVGs) in spatially-resolved transcriptomics data

raisin

scDD

R package to identify genes with differential distributions in single-cell RNA-seq

scRecover

Modest imputation for single-cell RNA-seq data. Homepage: https://miaozhun.github.io/scRecover. Bioconductor page: https://bioconductor.org/packages/scRecover.

Smmit

softImpute

:exclamation: This is a read-only mirror of the CRAN R package repository. softImpute — Matrix Completion via Iterative Soft-Thresholded SVD

tradeSeq

TRAjectory-based Differential Expression analysis for SEQuencing data

Viral-Track

z

z - jump around

zji90.github.io

website