☆46May 17, 2022Updated 3 years ago
Alternatives and similar repositories for batchbench
Users that are interested in batchbench are comparing it to the libraries listed below
Sorting:
- Methods to compute Local Inverse Simpson's Index (LISI)☆76Sep 2, 2021Updated 4 years ago
- An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.☆170Jan 26, 2024Updated 2 years ago
- Compendium to "A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines"☆55Feb 15, 2021Updated 5 years ago
- R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets☆246Mar 8, 2026Updated last week
- General notes and resources on how to analyze Spatial Transcriptomics data☆12Jun 20, 2023Updated 2 years ago
- Algorithm for the inference of cell types and lineage trees from single-cell RNA-seq data. This is a novel R package of the RaceID3 and S…☆44Nov 25, 2024Updated last year
- ☆56Dec 13, 2020Updated 5 years ago
- Simple simulation of single-cell RNA sequencing data☆233Jan 12, 2026Updated 2 months ago
- scRNA-seq clustering, visualization, and differential expression pipeline from Sims Lab papers☆22Sep 28, 2021Updated 4 years ago
- An R-based interface for loom files☆68Jul 9, 2020Updated 5 years ago
- ☆17Sep 20, 2020Updated 5 years ago
- Deep Embedding for Single-cell Clustering☆89Apr 9, 2024Updated last year
- A library for the deconvolution of bulk cell samples using single-cell RNA expression data.☆23Nov 3, 2021Updated 4 years ago
- R package for integrating and analyzing multiple single-cell datasets☆427Feb 4, 2026Updated last month
- Supporting material for publication: "Ovarian cancer mutational processes drive site-specific immune evasion"☆24May 10, 2025Updated 10 months ago
- Simplify functional enrichment results☆124Jan 30, 2026Updated last month
- DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…☆118Jan 22, 2024Updated 2 years ago
- R package for computation of (adjusted) rand-index and other such scores☆27Nov 25, 2025Updated 3 months ago
- Data and analysis for the Splatter paper☆29Dec 4, 2017Updated 8 years ago
- Interfaces for HDF5-based Single Cell File Formats☆175Nov 4, 2023Updated 2 years ago
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆317Nov 1, 2022Updated 3 years ago
- Highly scalable integration and classification of single-cell RNA sequencing data☆11Dec 27, 2020Updated 5 years ago
- Classification of Single cells by Transfer Learning☆10Oct 11, 2025Updated 5 months ago
- ☆12Jul 13, 2018Updated 7 years ago
- Panoramic stitching of single cell data☆297Jul 14, 2025Updated 8 months ago
- Analysis steps to calculate RNA Velocity in Bulk RNA-Seq samples. Step by Step Guide.☆17Jan 7, 2020Updated 6 years ago
- scover☆24Nov 3, 2023Updated 2 years ago
- Fast, sensitive and accurate integration of single-cell data with Harmony☆623Oct 10, 2025Updated 5 months ago
- Multi-modal single cell analysis pipelines☆62Dec 11, 2025Updated 3 months ago
- A tool for semi-automatic cell type harmonization and integration☆119Mar 9, 2026Updated last week
- ☆52Nov 28, 2025Updated 3 months ago
- Accurate, deep, fast, and fully-automated scRNA-seq cell-type annotation☆14Jan 21, 2025Updated last year
- ☆11May 3, 2022Updated 3 years ago
- Spatial Transcriptomics Capture Location Deconvolution☆203Oct 20, 2025Updated 5 months ago
- Create PyTorch Datasets from AnnData☆21Jan 6, 2026Updated 2 months ago
- Multiome GRN inference.☆133Apr 19, 2024Updated last year
- Snakemake pipeline that works with the scIB package to benchmark data integration methods.☆82Jan 23, 2025Updated last year
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆422Updated this week
- Automated, probabilistic assignment of cell types in scRNA-seq data☆212Jan 9, 2023Updated 3 years ago