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scrna-seq-analysis

Here are 138 public repositories matching this topic...

hemberg-lab / scRNA.seq.course

Analysis of single cell RNA-seq data course

r course sequencing bookdown scrna-seq scrna-seq-analysis

Updated Apr 11, 2022
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zhanghao-njmu / SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

scrna-seq shiny-apps single-cell shinyapps single-cell-genomics single-cell-rna-seq single-cell-analysis single-cell-atac-seq seurat single-cell-omics scrna-seq-analysis single-cell-sequencing shiny-app scanpy scatac-seq anndata scrna-pipeline seurat-objects single-cell-pipeline

Updated May 21, 2024
R

genecell / single-cell-papers-with-code

Papers with code for single cell related papers

reproducible-research reproducible-science scrna-seq single-cell single-cell-atac-seq single-cell-omics scrna-seq-analysis paper-with-code

Updated Jul 14, 2023

dpeerlab / Palantir

Single cell trajectory detection

markov-chain dimensionality-reduction scrna-seq trajectory-generation diffusion-maps differentiation manifold-learning single-cell-genomics cell-fate-transitions scrna-seq-analysis

Updated Nov 30, 2024
Jupyter Notebook

wheaton5 / souporcell

Clustering scRNAseq by genotypes

bioinformatics genomics computational-biology scrna-seq scrnaseq scrna-seq-analysis

Updated Nov 15, 2024
Python

juexinwang / scGNN

scGNN (single cell graph neural networks) for single cell clustering and imputation using graph neural networks

single-cell scrna-seq-analysis graph-neural-network

Updated Jul 25, 2024
Python

KrishnaswamyLab / MELD

Quantifying experimental perturbations at single cell resolution

machine-learning scrna-seq-analysis

Updated Sep 27, 2024
Python

AntonioDeFalco / SCEVAN

R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.

scrna-seq single-cell copy-number-variation copynumber tumor-evolution tumor-heterogeneity aneuploidy scrna-seq-analysis subclone-identification tumor-classification clonal-evolution scrna-pipeline subclonal-deconvolution microenvironment clonal-analysis

Updated Jun 11, 2024
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GfellerLab / SuperCell

Coarse-graining of large single-cell RNA-seq data into metacells

r-package scrna-seq-data coarse-graining scrna-seq-analysis

Updated Aug 29, 2024
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BaderLab / scClustViz

Explore and share your scRNAseq clustering results

r ui shiny scrna-seq single-cell differential-expression clustering-evaluation scrnaseq scrna-seq-analysis

Updated Sep 6, 2023
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dpeerlab / Harmony

Harmony framework for connecting scRNA-seq data from discrete time points

scrna-seq mnn batch-correction scrna-seq-analysis developmental-trajecotries

Updated Jul 13, 2024
Jupyter Notebook

jyyulab / NetBID

Data-driven Network-based Bayesian Inference of Drivers

bayesian-inference r-package network-analysis rna-seq-analysis scrna-seq-analysis

Updated Dec 21, 2024
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quon-titative-biology / scAlign

A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches

scrna-seq single-cell single-cell-genomics scrna-seq-analysis human-cell-atlas

Updated Nov 16, 2021
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jaleesr / BITFAM

BITFAM is a Bayesian approach and platform to infer transcription factor activities within individual cells using single cell RNA-sequencing data. Please see Gao S et al., Genome Research (2021) https://genome.cshlp.org/content/31/7/1296 for details.

transcription-factors rna-seq r scrna-seq bayesian-inference single-cell scrna-seq-analysis scrnaseq-data

Updated Feb 13, 2023
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ejohnson643 / EMBEDR

Statistical quality evaluation of dimensionality reduction algorithms

high-dimensional-data dimensionality-reduction dimension-reduction scrna-seq-analysis high-dimension-visualization

Updated Aug 21, 2023
Jupyter Notebook

paulranum11 / SPLiT-Seq_demultiplexing

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

scrna-seq single-cell fastq demultiplexing single-cell-rna-seq single-cell-analysis single-cell-omics scrna-seq-analysis single-cell-sequencing split-seq

Updated Oct 4, 2023
Python

fabilab / northstar

Single cell type annotation guided by cell atlases, with freedom to be queer

clustering scrna-seq singlecell scrna-seq-analysis cell-atlas leidenalg

Updated Jul 25, 2022
Python

IMB-Computational-Genomics-Lab / ascend

R package - Analysis of Single Cell Expression, Normalisation and Differential expression (ascend)

r scrnaseq singlecell scrna-seq-analysis rpackages

Updated Aug 28, 2019
R

maclean-lab / RVAgene

Recurrent Variational Auto gene encoder

rnn vae gene-expression-profiles scrna-seq-analysis

Updated Jan 12, 2023
Jupyter Notebook

mckellardw / scMuscle

The Cornell Single-Cell Muscle Project (scMuscle) aims to collect, analyze and provide to the research community skeletal muscle transcriptomic data

scrna-seq-data scrna-seq-analysis scrna-pipeline

Updated Nov 30, 2022
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