GitHub topics: scrna-seq-analysis
tarot0410/BREMSC
Novel joint clustering method with scRNA-seq and CITE-seq data
Language: R - Size: 30.6 MB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 6 - Forks: 3
HectorRDB/NationalAssembly
A short tutorial to help beginners in biostatistics and genomics understand an usual single-cell RNA-sequencing workflow
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RageScripter/Single-Cell-RNAseq
Single Cell RNAseq Analysis of lung tissue in mice
Language: R - Size: 23.4 KB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
hamidghaedi/scRNA_seq-analysis
scRNA analysis of public dataset on bladder cancer
Size: 95.3 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 3
FraserSingh/Scratch_space_scripts
Scripts from my Master's Dissertation on the UoE supercluster. Work in progress
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IDG-Kinase/HCA_Kinase_Analysis
Analysis of HCA Preview Data
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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
Language: R - Size: 5.18 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 32 - Forks: 12
chaitrasarathy/scRNAseq-with-seurat
Generic pipeline to analyse scRNAseq data using Seurat
Language: R - Size: 25.4 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0
kimberle9/rfca
R package: {rfca} Random forest-based cell annotation methods for scRNAseq analysis. {rfca} contains methods which identifies cell types using machine learning trained on a diversity of cell types, without the need for a labelled training dataset. It also allows you to train your own cell prediction models with your own labels (cell type, subtype, cell state, cluster number etc). This package is best suited for researchers who want to annotate their datasets in a quick and unbiased way, phenotype their datasets based on cell identity proportions, and discover common cell states across different datasets and disease models.
Language: R - Size: 155 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 1
arcotan/single-cell-data-analysis
🧫 Comparison between COTAN and state of the art libraries for the analysis of scRNA-seq data.
Language: Jupyter Notebook - Size: 352 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
theislab/HPA_reproducibility
Reproducible code for the scRNA-seq analyses in the paper 'The neuroendocrine response to stress at single-cell resolution" by Lopez et al. 2020.
Language: Jupyter Notebook - Size: 120 MB - Last synced at: 6 months ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 1
mckellardw/scMuscle
The Cornell Single-Cell Muscle Project (scMuscle) aims to collect, analyze and provide to the research community skeletal muscle transcriptomic data
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sarwarchy20/scAnalyzeR
a comprehensive software package with graphical user interface for single-cell RNA sequencing analysis.
Language: R - Size: 23.2 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0
danieljgorski/scRNAseq-Hmmr-OE
Hyaluronan Mediated Motility Receptor (Hmmr) overexpression
Language: R - Size: 32 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0
GCS-ZHN/scPert
Folded and map strategy and cell perturbation response prediction
Language: Python - Size: 5.5 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 1
sxtforreal/Tensor_scRNA-seq
Leveraged tensor-based statistical methods on single-cell RNA-sequencing datasets to predict the progression stage of Covid-19
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JarningGau/ZFP541_manuscript
Source codes for ZFP541 manuscript
Language: Shell - Size: 709 KB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 1
doerlbh/scTSA
Single-Cell Topological Simplicial Analysis (scTSA)
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JackSSK/Ageas
AutoML-based Genetic regulatory Element extrAction System
Language: Python - Size: 752 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 4 - Forks: 1
maclean-lab/RVAgene
Recurrent Variational Auto gene encoder
Language: Jupyter Notebook - Size: 32.7 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 14 - Forks: 4
MichaelPeibo/mDA-time-course-scRNA-seq
This is private analysis pipeline for time course scRNA-seq data of mesencephalic dopaminergic neuron differentiation in vitro
Language: R - Size: 31.9 MB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0
juliendelile/Antler
R package for single-cell RNA-sequencing analysis
Language: R - Size: 157 MB - Last synced at: over 2 years ago - Pushed at: about 4 years ago - Stars: 11 - Forks: 1
Sarah145/batch_correct
Comparison of batch correction methods for scRNA-seq data - basically a clone of BatchBench
Language: R - Size: 214 KB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 1
thimler/SCRNAseq
Gene set enrichment analysis from scRNA seq data : in search of the original tissue
Language: R - Size: 7.18 MB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0
milescsmith/SeuratPlotly
Plot_ly-based plotting functions for use with Seurat objects
Language: R - Size: 2.33 MB - Last synced at: over 2 years ago - Pushed at: about 6 years ago - Stars: 2 - Forks: 2
milescsmith/ViolinEnsemble
Create violin plots of gene expression for multiple genes
Language: R - Size: 345 KB - Last synced at: over 2 years ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0
asifzubair/deconR
R package for Bayesian deconvolution of bulk RNAseq data
Language: C++ - Size: 5.73 MB - Last synced at: almost 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
DominiquePaul/Optimised-skin-cell-protocol-scRNA
Code for the paper "An optimized tissue dissociation protocol for single cell RNA sequencing analysis of fresh and cultured human skin biopsies""
Language: R - Size: 756 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
himelmallick/BenchmarkSingleCell
Large-scale Benchmarking of Single-cell Differential Expression Analysis Methods
Language: R - Size: 16.9 MB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0
Manu-1512/Matt_et_al_2021
Simultaneous analysis of genes and transposable elements (TEs) from 10X scRNAseq datasets derived from CD and NIBD samples using Alevin.
Language: R - Size: 58.6 KB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0
soymintc/scBSC
Calculate spatial correlation between two genes of a Seurat-format spatial scRNA-seq data
Language: R - Size: 1.43 MB - Last synced at: over 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0
ngshasan/scRNA-marker-gene-Annotation
scRNA-marker-gene-Annotation.
Language: R - Size: 12.7 MB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 1
ngshasan/single-cell-RNA-Seq-Data-Analysis-Methods
single-cell-RNA-Seq-Data-Analysis-Methods
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dmalzl/yoRISC
A bit of code to interconvert objects between the Seurat and RISC environments for scRNA-seq data analysis
Language: R - Size: 13.7 KB - Last synced at: 3 months ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0
Munfred/wormcells-data
Gene expression on C. elegans single cells
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milescsmith/ReducedHeat
Display gene expression along a given reduced dimension on a heatmap
Language: R - Size: 59.6 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 0
aosakwe/HGEN396-Analysis-Scripts
R Scripts used in scRNA-seq analysis of T2D Islets
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rfechtner/pypairs
PyPairs - A python scRNA-Seq classifier
Language: Python - Size: 155 MB - Last synced at: 26 days ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 4
inuritdino/HyperInflamDataProcessing
scRNA-seq datasets to support Jung et al, Sci Adv, 7(6): eabe5735, 2021. DOI: 10.1126/sciadv.abe5735
Language: R - Size: 168 KB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
ethan-mccarthy/scrnahelper
I've written a few functions that help me look through scRNA-seq data while working with Seurat.
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rahulbhadani/scomix
Single-Cell Data Science
Language: Python - Size: 99.6 KB - Last synced at: 27 days ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
Sarah145/MSc_Project
Work for my MSc thesis - 'Characterising transcriptional variation in tissue-resident macrophage subsets using sc-RNA-seq'
Language: Python - Size: 12.9 MB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0
ucdavis-bioinformatics-training/So-you-want-to-do-a-Single-Cell-RNA-seq-experiment
So you want to do a: Single Cell RNA-seq experiment
Size: 15.3 MB - Last synced at: over 2 years ago - Pushed at: over 7 years ago - Stars: 2 - Forks: 4
gtca/echinus
Get a gene expression table from transcript compatibility counts
Language: Go - Size: 629 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
llrs/BaseSet_scRNAseq
Examples of methods for scRNAseq that might benefit from BaseSet
Size: 18.2 MB - Last synced at: 27 days ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
milescsmith/AutoImpute Fork of divyanshu-talwar/AutoImpute
An autoencoder based imputation of the sparse single cell RNA-seq data.
Language: Python - Size: 705 KB - Last synced at: over 2 years ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0