scrna-seq-data

Here are 23 public repositories matching this topic...

seandavi / awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

python bioinformatics clustering gene-expression data-visualization dimensionality-reduction awesome-list data-integration atac-seq single-cell rna-seq-data scrna-seq-data cell-differentiation gene-expression-profiles analysis-pipeline spatial-transcriptomics cell-populations rna-seq-experiments cell-clusters

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nsalomonis / altanalyze

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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.

python bam-files clustering graphical-interface pagerank bioinformatics-pipeline alternative-splicing command-line-tool splicing-quantification network-analysis pathway-analysis rna-seq-data scrna-seq-data cell-cycle cell-type-classification splicing-visualization fastq-anaysis single-cell-splicing marker-gene-analysis louvain-community-detection

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Python

GfellerLab / SuperCell

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

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

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R

randel / MIND

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Using Bulk Gene Expression to Estimate Cell-Type-Specific Gene Expression via Deconvolution

scrna-seq-data bulk-gene-expression

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HTML

oscar-franzen / PanglaoDB

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metadata and data from the database

scrna-seq scrna-seq-data

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mckellardw / scMuscle

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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

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HTML

multitalk / miRTalk

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Extracellular vesicle-derived miRNA-mediated cell-cell communication inference for single-cell transcriptomic data

scrna-seq-data mirna single-cell-rna-seq exosomes extracellular-vesicles cell-cell-interaction cell-cell-communication microvesicles

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HTML

ankitbioinfo / nico_tutorial

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A package that performs cell type annotations on single cell resolution of spatial transcriptomics data, find the niche interactions and statistically enriched covariation of gene programs between interacting cell types from the neighborhood.

scrna-seq scrna-seq-data scrnaseq nico scrna-seq-analysis spatial-transcriptomics niche-modelling merfish seqfish niche-covariation

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Jupyter Notebook

AllenInstitute / tasic2016data

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Single cell transcriptomic data from Tasic, et al. (2016)

transcriptomics scrna-seq-data scrattch

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R

nlawlor / V-SVA

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V-SVA: An R Shiny application for detecting and annotating hidden sources of variation in single cell RNA-seq data

visualization r shiny transcriptomics scrna-seq-data single-cell-rna-seq surrogate-variable-analysis

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R

umangv / picturedrocks

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PicturedRocks Single Cell Analysis Tool

python scrna-seq single-cell scrna-seq-data university-of-michigan

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Python

Gina727 / scRNA-seq-analyst

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ScRNA-seq Analysis Copilot serves as an interactive agent to learn single cell sequencing, answering questions and helping new learners to practice analysis.

api ai scrna-seq scrna-seq-data scrna-seq-analysis chatgpt

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R

DaminK / GlobalGround-MetricLearning

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Python implementation of the AISTATS2025 paper "Global Ground Metric Learning with Applications to scRNA data" by Damin Kühn nad Michael T. Schaub. To use GGML on your own data, refer to the python package below:

genomics metric-learning optimal-transport scrna-seq-data global-metrics