chenzhen's repositories
SCpubr
Generate high quality, publication ready visualizations for single cell transcriptomics data.
scirpy
A scanpy extension to analyse single-cell TCR and BCR data.
knowledgebase
recipes that save time
voyager
From geospatial to spatial -omics
ktplotspy
Python library for plotting Cellphonedb results. Ported from ktplots R package.
ktplots
Some tools for plotting single-cell data
SuperCell
Coarse-graining of large single-cell RNA-seq data into metacells
dandelion
dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
AfteReset
AfteReset
glmGamPoi
Fit Gamma-Poisson Generalized Linear Models Reliably
scRNA-seq_notes
A list of scRNA-seq analysis tools
hdWGCNA
High dimensional weighted gene co-expression network analysis
STdeconvolve
Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
GSVA
Gene set variation analysis
sccomp
Testing differences in cell type proportions from single-cell data.
single-cell-best-practices
https://www.sc-best-practices.org
miloR
R package implementation of Milo for testing for differential abundance in KNN graphs
MEBOCOST
A python-based package and software to predict metabolite mediated cell-cell communications by single-cell RNA-seq data
SEraster
Spatial Experiments raster - a rasterization preprocessing framework for scalable spatial omics data analysis
ctwas
package for the causal TWAS project
xCell
Cell types enrichment analysis
CuratedAtlasQueryR
Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.
TCR-BCR-seq-analysis
T/B cell receptor sequencing analysis notes
SimpleELN-Personal
An electronic lab notebook (ELN software) designed to facilitate the secure and efficient organization, storage, search, and sharing of scientific data and research notes.
sdmTMB
:earth_americas: An R package for spatial and spatiotemporal GLMMs with TMB