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.​​

Musicatk

musicatk (Mutational Signature Comprehensive Analysis Toolkit) is a comprehensive toolkit for analysis of mutational signatures. It has utilities for extracting variants from a variety of file formats, contains multiple methods for discovery of novel signatures or prediction of known signatures, as well as many types of downstream visualizations for exploratory analysis. This package has the ability to parse and combine multiple motif classes in the mutational signature discovery or prediction processes. Mutation motifs include single base substitutions (SBS), double base substitutions (DBS), insertions (INS) and deletions (DEL).

ExperimentSubset

ExperimentSubset is an R package to manage subsets of Bioconductor Experiment objects. ExperimentSubset package enables users to perform flexible subsetting of Single-Cell data that comes from the same experiment as well as the consequent storage of these subsets back into the same object. In general, it offers the same interface to the users as the any of the input *Experiment object such SummarizedExperiment, RangedSummarizedExperiment and SingleCellExperiment while imparting the additional subsetting features.