popsicleR, a flexible R package aimed at providing most of the necessary quality controls and preliminary information for complete and detailed analysis of single cell RNA-seq data.
☆23Dec 3, 2025Updated 3 months ago
Alternatives and similar repositories for popsicleR
Users that are interested in popsicleR are comparing it to the libraries listed below
Sorting:
- Code related to scRNA analysis using the scAmpi workflow☆27Jan 21, 2026Updated last month
- An R package to implement Differential Gene Set Enrichment Analysis (DGSEA): A statistical approach to quantify the relative enrichment o…☆14Apr 12, 2023Updated 2 years ago
- ☆12Oct 31, 2020Updated 5 years ago
- Shareable project for: Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States☆10Nov 11, 2020Updated 5 years ago
- ☆11Nov 7, 2022Updated 3 years ago
- Single-cell Consensus Clusters of Encoded Subspaces☆14Aug 14, 2023Updated 2 years ago
- Single-cell RNA-seq data-based inference of multilayer inter- and intra-cellular signaling networks☆29Aug 16, 2021Updated 4 years ago
- Calculating Tumor microenvironment score☆29Jan 20, 2023Updated 3 years ago
- Do microbiome analysis with dada2 and phyloseq object☆14Oct 9, 2024Updated last year
- Function Enrichment analysis and Network construction☆14Dec 10, 2025Updated 2 months ago
- Code used for muti cellular factor analysis☆16Dec 13, 2023Updated 2 years ago
- GREAT algorithm in Python☆14Oct 24, 2022Updated 3 years ago
- ☆12Jan 8, 2026Updated 2 months ago
- Accurate, deep, fast, and fully-automated scRNA-seq cell-type annotation☆14Jan 21, 2025Updated last year
- ☆30Jul 8, 2018Updated 7 years ago
- CellNeighborEX: Deciphering Neighbor-Dependent Gene Expression from Spatial Transcriptomics Data☆16Jul 10, 2024Updated last year
- ☆18Jun 13, 2024Updated last year
- Quantifying metabolism activity at the single-cell resolution☆153Feb 18, 2026Updated 2 weeks ago
- represent each cell in UMAP plots as a pie chart☆16Sep 27, 2021Updated 4 years ago
- R markdown notebooks for the Tabula Muris network analysis in Iacono et al. (2019)☆12Jun 30, 2021Updated 4 years ago
- Vaeda method for computational doublet annotation☆19Feb 1, 2026Updated last month
- A unified downloader+preprocessor for cancer genomics datasets☆16Apr 7, 2024Updated last year
- Gene Expression Decomposition and Integration☆19Feb 9, 2026Updated 3 weeks ago
- ☆39Aug 4, 2021Updated 4 years ago
- ☆113Nov 12, 2022Updated 3 years ago
- 📊 An R package for interactively exploring UCSC Xena https://xenabrowser.net/datapages/; Book: https://lishensuo.github.io/UCSCXenaShiny…☆104Feb 8, 2026Updated last month
- ☆22Nov 9, 2023Updated 2 years ago
- ☆15Apr 2, 2023Updated 2 years ago
- Marker gene selection from scRNA-seq data☆16Sep 15, 2020Updated 5 years ago
- Trajectory inference and differential expression over multiple conditions in scRNA-seq☆26Apr 22, 2021Updated 4 years ago
- pytorch dataloaders for single-cell perturbation data☆43Feb 27, 2026Updated last week
- A tool for removing doublets from single-cell RNA-seq data☆75Dec 2, 2020Updated 5 years ago
- ☆18Oct 4, 2022Updated 3 years ago
- Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data☆238May 8, 2023Updated 2 years ago
- Public code repository for the Banovich Lab at the Translational Genomics Research Institute (TGen).☆49Feb 9, 2024Updated 2 years ago
- Pipeline for SpatialTranscriptomics and 10X Visium data☆21Jul 22, 2025Updated 7 months ago
- Multi-Omics integration and VIsualization in Cancer Subtyping☆146Jul 19, 2021Updated 4 years ago
- A collection of tumour microenvironment single-cell RNA sequencing datasets for use in R and other pipelines.☆19Jul 28, 2025Updated 7 months ago
- A software package for connecting cell level features in single cell RNA sequencing data with receptor ligand activity. Please be aware t…☆19Dec 5, 2024Updated last year