cell-type-classification

There are 0 repository under cell-type-classification topic.

Teichlab / celltypist
A tool for semi-automatic cell type classification
python single-cell machine-learning scrna-seq cell-type-classification label-transfer
Language:Python 424
rezakj / iCellR
iCellR is an interactive R package designed to facilitate the analysis and visualization of high-throughput single-cell sequencing data. It supports a variety of single-cell technologies, including scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq, and Spatial Transcriptomics (ST).
10xgenomics 3d batch-normalization cell-type-classification cite-seq clustering clustering-algorithm diffusion-maps dropout icellr imputation intractive-graph normalization pseudotime scrna-seq scvdj-seq singel-cell-sequencing umap
Language:R 124
ZJUFanLab / scDeepSort
Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network
annotation cell-type-classification deep-learning gnn graph-neural-network reference-free scrna-seq single-cell transcriptomics
Language:Python 106
nsalomonis / altanalyze
AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.
rna-seq-data alternative-splicing scrna-seq-data bioinformatics-pipeline clustering pathway-analysis network-analysis splicing-quantification splicing-visualization python fastq-anaysis bam-files single-cell-splicing cell-cycle cell-type-classification marker-gene-analysis graphical-interface command-line-tool pagerank louvain-community-detection
Language:Python 105
deweylab / CellO
CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology
bioinformatics cell-biology cell-type cell-type-classification computational-biology machine-learning ontologies rna-seq single-cell-rna-seq
Language:Jupyter Notebook 67
CahanLab / CellNet
CellNet: network biology applied to stem cell engineering
rna-seq cell-type-classification stem-cell-differentiation
Language:R 54
ruiyi-zhang / scPretrain
scPretrain: Multi-task self-supervised learning for cell type classification
self-supervised-learning cell-type-classification single-cell-analysis multi-task-learning
Language:Python 23
CahanLab / PySingleCellNet
singleCellNet in Python
cell-annotation cell-type-classification single-cell cell-typing
Language:Python 15
LucasESBS / scoreCT
scoreCT: Automated Cell Type Annotation
cell-type-classification single-cell
Language:Jupyter Notebook 15
clustermole
igordot / clustermole
Unbiased single-cell transcriptomic data cell type identification
cell-type cell-type-annotation cell-type-classification cell-type-identification cell-type-matching gene-expression-signatures scrna-seq single-cell
Language:R 14
Cellcano
marvinquiet / Cellcano
Supervised cell type identification for scATAC-seq data
bioinformatics cell-type-classification cell-type-identification celltype-annotation single-cell supervised-classification-methods
Language:Python 13
ZJUFanLab / scDeepSort_performance_comparison
The source code and results for different methods on annotating external testing datsets of human and mouse.
deep-learning annotation scrna-seq transcriptomics single-cell cell-type-classification graph-neural-network reference-free gnn
Language:R 12
biomed-AI / SANGO
The official implementation for "SANGO".
bioinformatics cell-type-annotation cell-type-classification cell-type-identification sequence single-cell supervised-classification-methods
Language:Jupyter Notebook 8
CimpleG
CostaLab / CimpleG
CimpleG, an R package to find (small) CpG signatures.
methylation deconvolution cpg-signature biomarker-discovery biomarkers cell-type-classification r
Language:R 6
scMKL
ohsu-cedar-comp-hub / scMKL
Python package for single-cell analysis with multiple kernel learning.
analysis cell-type-classification kernel-learning multiomics single-cell
Language:Jupyter Notebook 6
ACDBio / GCDPipe
A pipeline to predict risk genes, implicated cell types and drugs for repurposing based on known risk genes (derived from GWAS) for complex traits.
cell-type-classification cell-type-gene-expression-analysis cell-type-matching drug-discovery drug-repurposing genomics gwas gwas-pipeline machine-learning alzheimers-disease disease-prediction diseases irritable-bowel-syndrome schizophrenia inflammatory-bowel-disease
Language:Python 3
fungenomics / scCoAnnotate
Pipeline for consensus prediction of cell types in single-cell RNA sequencing data.
cell-type-classification reproducible-research single-cell single-cell-rna-seq snakemake-workflow
Language:R 3
edmerix / UnitSubclassify
GUI for semi-automatic single neuron classification by cell type
spike-sorting neuroscience neurons cell-type-classification matlab matlab-gui
Language:MATLAB 2
WangLab-SINH / BrainCellR
An R package for cell type nomenclature
cell-type-classification machine-learning single-cell
Language:R 0
adabyt / scrnaseq_analysis_project
Single-cell RNA-seq analysis project for learning purposes.
anndata bioinformatics biological-data immunology jupyter-notebook leiden matplotlib numpy pandas python scanpy scikit-learn scrnaseq single-cell 10xgenomics clustering dimensionality-reduction machine-learning visualization cell-type-classification
Language:Jupyter Notebook
ajitjohnson / IMAAP
Annotation and Analysis of Multiplexed Imaging Data
imaging-informatics cell-type-classification cycif
Language:R
birchgit / SingleCell_type
Code for the Systems Biology: Computational Analysis and Interpretation of High-throughput Data course at HU Berlin.
multiclass-classification single-cell-rna-seq cell-type-classification dnn xgboost
Language:Jupyter Notebook
Geoff-Dilly / GD_scRNA_Pipeline
R pipeline for reliably and reproducably analyzing scRNAseq experiments using Seurat and associated tools.
bioinformatics cell-type-classification scrna-seq
Language:R
Geoff-Dilly / Run_Cell_Type_Mapper
Small repo for running Allen Institute's Cell_Type_Mapper (MapMyCells) on Seurat scRNAseq objects.
bioinformatics cell-type-classification scrna-seq
Language:Shell
lubianat / wiki_vickaryous
A Flask app for the Vickaryous & Hall 2006 cell type classification
cell-type-classification wikidata
Language:HTML