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PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please report only **technical issues** on this repository (e.g., compiling, programs a…
BootStrap on Seurat (single cell object) to evaluate cluster stability.
R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
An R package for learning complex single cell trajectory and expression trends
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 StemID2 method including novel functionalities and performanc…
Pathway-based trajectory inference method for time-series scRNAseq data
Program to run the SOWH test (likelihood-based test used to compare tree topologies which are not specified a priori)
Pilon is an automated genome assembly improvement and variant detection tool
FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries
R package for detecting doublets in single-cell RNA sequencing data
Code for the empty droplet and cell detection project from the HCA Hackathon.
Clone of the Bioconductor repository for the DropletUtils package.
Computational correction of copy-number effect in CRISPR-Cas9 essentiality screens
Single RNA-seq data analysis with R (Finland, May, 2019)
Fast, sensitive and accurate integration of single-cell data with Harmony
A benchmark of batch-effect correction methods for single-cell RNA sequencing data
The following code accompanies a manuscript combining single-cell RNA-sequencing and genotyping to analyze cellular hierarchies in acute myeloid leukemia (AML).
r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)
Multi-study integration of cellular trajectories
Software for clustering de novo assembled transcripts and counting overlapping reads