zhenweiqian

rhea

Recognizing HGT Events in Assemblies

DiffSided_CRC_SCseq

CountCorrect

CountCorrect: Background removal for Nanostring WTA data

SpaCET

Spatial Cellular Estimator for Tumors

CellRef

Guided construction of single cell reference

arriba

Fast and accurate gene fusion detection from RNA-Seq data

cellrank

CellRank: dynamics from multi-view single-cell data

StemID

Algorithm for the inference of cell types and lineage trees from single-cell RNA-seq data.

stemi_mofa

Multiomics factor analysis of STEMI patients

metagenome_MM_code

Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen recycling bacteria

noisyR

Package documentation and examples:

bulkAnalyseR

ClustAssess

Tools for assessing clustering robustness

MASLD-NASH

scripts associated with NAFLD-NASH project

Cultivated-Gut-Fungi

Murase_2024_Nature

aavperturbseq

Massively parallel in vivo Perturb-seq

Kassandra

Bostongene cell deconvolution algorithm from RNAseq

LHRS

Low-heterogeneity risk stratification for prognostication in HCC

scRank

A computational method to rank and infer drug-responsive cell population towards in-silico drug perturbation using a target-perturbed gene regulatory network (tpGRN) for single-cell transcriptomic data

GAGE-seq

Data processing and analysis workflow for GAGE-seq, a coassay of single-cell HiC and single-cell RNA-seq

als_scrnaseq

Figure codes for the manuscript: T cell responses at diagnosis of amyotrophic lateral sclerosis predict disease progression

EasyMetagenome

Easy Metagenome Pipeline

biobakery

bioBakery tools for meta'omic profiling

cmseq

Set of utilities on sequences and BAM files

R-script-for-scRNA-seq-analysis

SGVFinder

IGI-DL

Code for ST_IGI package

circadian_immune_mouse_melanoma

pixelator

A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) assays.