Software

Software

Celda

"Celda" stands for "CEllular Latent Dirichlet Allocation". It is a suite of Bayesian hierarchical models and supporting functions to perform bi-clustering of features and cells for single-cell genomic data. This algorithm is an extension of the Latent Dirichlet Allocation (LDA) topic modeling framework that has been popular in text mining applications.

DecontX

DecontX is a Bayesian hierarchical model to estimate and remove cross-contamination from ambient RNA in single-cell genomic data. DecontX will take the count matrix, estimate the contamination levels within each individual cell, and deliver a decontaminted count matrix for downstream analysis.

Scruff

scruff (Single Cell RNA-Seq UMI Filtering Facilitator) is a package for processing single cell RNA-seq (scRNA-seq) FASTQ reads generated by CEL-Seq and CEL-Seq2 protocols. It demultiplexes scRNA-seq FASTQ files, aligns reads to reference genome using Rsubread, and generates UMI filtered count matrix.​​