RNA sequencing (RNA-seq) is widely used to identify differentially expressed genes (DEGs) and reveal biological mechanisms underlying complex biological processes. RNA-seq is often performed on...
Read More »circRNAprofiler – an R-based computational framework for the downstream analysis of circular RNAs
Circular RNAs (circRNAs) are a newly appreciated class of non-coding RNA molecules. Numerous tools have been developed for the detection of circRNAs, however computational tools to perform downstream...
Read More »TEffectR – an R package for studying the potential effects of transposable elements on gene expression
Recent studies highlight the crucial regulatory roles of transposable elements (TEs) on proximal gene expression in distinct biological contexts such as disease and development. However, computational tools...
Read More »CAGEfightR – analysis of 5′-end data using R/Bioconductor
5′-end sequencing assays, and Cap Analysis of Gene Expression (CAGE) in particular, have been instrumental in studying transcriptional regulation. 5′-end methods provide genome-wide maps of...
Read More »BgeeDB – an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests
Researchers from University of Lausanne have developed BgeeDB, a collection of functions to import into R re-annotated, quality-controlled and reprocessed expression data available in the Bgee database. This includes data from thousands of...
Read More »Trendy – segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments
High-throughput expression profiling experiments with ordered conditions (e.g. time-course or spatial-course) are becoming more common for studying detailed differentiation processes or spatial patterns. Identifying dynamic changes at both the individual gene and whole transcriptome level can provide...
Read More »SC2P – two-phase differential expression analysis for single cell RNA-seq
Single-cell RNA-sequencing (scRNA-seq) has brought the study of the transcriptome to higher resolution and makes it possible for scientists to provide...
Read More »clusterExperiment and RSEC – A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets
Clustering of genes and/or samples is a common task in gene expression analysis. The goals in clustering can vary, but an important scenario is that of...
Read More »atacR – a workflow for simplified analysis of ATAC-cap-seq data in R
Assay for Transposase-Accessible Chromatin (ATAC)-cap-seq is a high-throughput sequencing method that combines ATAC-seq with targeted nucleic acid enrichment of precipitated DNA fragments. There are increased analytical difficulties arising from working with a set of regions of interest that may be ...
Read More »CEMiTool – gene co-expression network analysis
The analysis of modular gene co-expression networks is a well-established method commonly used for discovering the systems-level functionality of genes. In addition, these studies provide a basis for the discovery of clinically relevant molecular pathways underlying different diseases and conditions. ...
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