Reconstruct the lineage topology of a scRNA-seq differentiation dataset.
☆19Jun 25, 2020Updated 5 years ago
Alternatives and similar repositories for merlot
Users that are interested in merlot are comparing it to the libraries listed below
Sorting:
- Regulatory networks with Direct Information☆17Oct 14, 2019Updated 6 years ago
- PRObabilistic Simulations of ScRNA-seq Tree-like Topologies☆26Jan 10, 2024Updated 2 years ago
- sake☆29Feb 8, 2023Updated 3 years ago
- ☆40Jun 25, 2025Updated 8 months ago
- ☆15Apr 3, 2025Updated 11 months ago
- Wishbone is an algorithm to align cells along developmental trajectories with branches☆42Feb 8, 2020Updated 6 years ago
- Regulatory networks with Direct Information in python☆40Mar 9, 2023Updated 3 years ago
- A software package for analyzing snapshots of developmental processes☆158Sep 15, 2022Updated 3 years ago
- psupertime is pseudotime ordering for single cell RNA-seq data with sequential labels☆48Jul 20, 2022Updated 3 years ago
- R package for the joint analysis of multiple single-cell RNA-seq datasets☆220Mar 9, 2026Updated last week
- An R package to perform systematic quality checks on comparative genomics analyses☆12Mar 5, 2026Updated 2 weeks ago
- This package removes unwanted variation from raw sequencing count data using Negative Binomial and/or Zero Inflated Negative Binomial mod…☆18Jun 13, 2024Updated last year
- Estimating gene family turnover rates by likelihood-based methods☆12Aug 17, 2020Updated 5 years ago
- A R package for integrated scRNA-seq data analysis using the RPCI algorithm☆44Mar 30, 2024Updated last year
- Scripts to run and benchmark scRNA-seq cell cluster labeling methods☆48May 23, 2020Updated 5 years ago
- notes and materials from dbug meetings☆10Sep 26, 2018Updated 7 years ago
- Feature Ranking in (possibly large) Clustered Single Cell Data☆41Apr 15, 2021Updated 4 years ago
- scMatch: a single-cell gene expression profile annotation tool using reference datasets☆21Aug 11, 2020Updated 5 years ago
- STRIDE: Species Tree Root Inference from Gene Duplication Events☆11Aug 28, 2018Updated 7 years ago
- Code for the MNN manuscript figures☆49Oct 1, 2018Updated 7 years ago
- Sparse Partial correlation ON Gene Expression - an R package for fast and robust ceRNA network inference☆14Nov 13, 2025Updated 4 months ago
- ☆39Aug 4, 2021Updated 4 years ago
- Multithreaded Gephi Force Atlas2 Layout in 2 or 3-d☆23May 8, 2020Updated 5 years ago
- Bioconductor package that makes BIG data pint-sized.☆21Feb 12, 2024Updated 2 years ago
- Digital Cell Sorter (DCS): single cell RNA-seq analysis toolkit. Documentation:☆24Jun 8, 2021Updated 4 years ago
- metadata and data from the database☆42Jan 29, 2020Updated 6 years ago
- Generate cellular maps of differentiation manifolds with complex topologies.☆27Jun 26, 2018Updated 7 years ago
- singleCellNet in Python☆15Feb 25, 2026Updated 3 weeks ago
- NaRnEA (Nonparametric analytical Rank-based Enrichment Analysis)☆11Mar 2, 2023Updated 3 years ago
- RNA velocity estimation in R☆196Sep 14, 2023Updated 2 years ago
- MICROPHERRET: MICRObial PHEnotypic tRait ClassifieR using machine lEarning Techniques☆12Dec 16, 2025Updated 3 months ago
- Web tool for exploring cell-cell ligand-receptor mediated communication networks☆23Aug 18, 2016Updated 9 years ago
- Exercises for training scientists to perform some RNA-seq analyses.☆11Oct 7, 2019Updated 6 years ago
- Pathway-based trajectory inference method for time-series scRNAseq data☆25May 18, 2021Updated 4 years ago
- Identify circular trajectories in scRNA-seq data using an autoencoder with sinusoidal activations☆24Dec 17, 2021Updated 4 years ago
- Downstream analysis script for sci-fate (TF-gene linkage analysis / cell linkage analysis)☆24Jan 22, 2020Updated 6 years ago
- Descriptive probabilistic marker gene approach to single-cell pseudotime inference☆30Nov 29, 2019Updated 6 years ago
- ☆29Feb 1, 2023Updated 3 years ago
- Beautify the phylogenetic tree using one Excel sheet only☆16Mar 2, 2024Updated 2 years ago