Z-YWJ's Stars
LinearDesignSoftware/LinearDesign
The LinearDesign mRNA design software.
CSOgroup/torchgmm
WangPeng-Lab/scGCO
Single-cell Graph Cuts Optimization
CSOgroup/cellcharter
A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
xzhoulab/SPARK
Spatially resolved transcriptomic analysis
jason-weirather/hla-polysolver
Fork of the Polysolver project
MathOnco/NeoPredPipe
Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.
s175573/GIANA
Ultrafast TCR clustering algorithm based on geometric isometry
liulab-dfci/TRUST4
TCR and BCR assembly from RNA-seq data
heilandd/SPTCR_seq_code
High-sensitive spatially resolved T cell receptor sequencing with SPTCR-seq
theMILOlab/SPATAImmune
theMILOlab/SPTCR-Seq-Pipeline
Pipeline to demultiplex, correct , annotate and UMI correct T-Cell Receptor Long Reads.
yuyang3/pan-B
These are scripts for pan-cacner B cells analyses.
almaan/star-repair
kharchenkolab/Baysor
Bayesian Segmentation of Spatial Transcriptomics Data
SydneyBioX/BIDCell
Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data
twbattaglia/tumor-microbiome
A pan-cancer analysis of the microbiome in metastatic cancer (Battaglia et. al, Cell, 2024)
TencentAILabHealthcare/spatialID
FredHutch/Galeano-Nino-Bullman-Intratumoral-Microbiota_2022
Analysis code used in Galeano Nino et al., Impact of Intratumoral Microbiota on Spatial and Cellular Heterogeneity in human cancer. 2022
JEFworks-Lab/MERINGUE
characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities
STOmics/SAW
STOmics/ST_BarcodeMap
KlugerLab/GeneTrajectory
R implementation of GeneTrajectory
liziyie/Onco-fetal-CAF-in-HCC
SydneyBioX/CellSPA
Cell Segmentation Performance Assessment
TAPE-Lab/Qin-CardosoRodriguez-et-al
Scripts and notebooks for Qin & Cardoso Rodriguez et al
SpatialTranscriptomicsResearch/std-poisson
Poisson regression for Spatial Transcriptomics data as described in Berglund et al. 2018
theislab/scib
Benchmarking analysis of data integration tools
carmonalab/ProjecTILs
Interpretation of cell states using reference single-cell maps
theislab/cellrank
CellRank: dynamics from multi-view single-cell data