nondetects

This package is intended to identify differentially expressed genes driven by Copy Number Alterations from samples with both gene expression and CNA data.

A pipeline which processes single cell RNA-seq (scRNA-seq) reads from CEL-seq and CEL-seq2 protocols. Demultiplex scRNA-seq FASTQ files, align reads to reference genome using Rsubread, and generate UMI filtered count matrix. Also provide visualizations of read alignments and pre- and post-alignment QC metrics.

Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way.

Low- and high-level wrappers for Gemma's RESTful API. They enable access to curated expression and differential expression data from over 10,000 published studies. Gemma is a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles.

scQTLtools is a comprehensive R/Bioconductor package that facilitates end-to-end single-cell eQTL analysis, from preprocessing to visualization

The package imports the result of tRNAscan-SE as a GRanges object.