BiocSet displays different biological sets in a triple tibble format. These three tibbles are element, set, and elementset. The user has the ability to activate one of these three tibbles to perform common functions from the dplyr package. Mapping functionality and accessing web references for elements/sets are also available in BiocSet.

This package exposes an annotation databases generated from UCSC by exposing these as TxDb objects.

This package provides R environments for the annotation of microarrays.

This package provides a computational method that infers copy number variations (CNV) in cancer scRNA-seq data and reconstructs the tumor phylogeny. It integrates signals from gene expression, allelic ratio, and population haplotype structures to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. It does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output). It can be used to:

1. detect allele-specific copy number variations from single-cells

2. differentiate tumor versus normal cells in the tumor microenvironment

3. infer the clonal architecture and evolutionary history of profiled tumors

For details on the method see Gao et al in Nature Biotechnology 2022.

Many methods allow us to extract biological activities from omics data using information from prior knowledge resources, reducing the dimensionality for increased statistical power and better interpretability. decoupleR is a Bioconductor package containing different statistical methods to extract these signatures within a unified framework. decoupleR allows the user to flexibly test any method with any resource. It incorporates methods that take into account the sign and weight of network interactions. decoupleR can be used with any omic, as long as its features can be linked to a biological process based on prior knowledge. For example, in transcriptomics gene sets regulated by a transcription factor, or in phospho-proteomics phosphosites that are targeted by a kinase.

This package is developed for the analysis and visualization of clonal tracking data. The required data is formed by samples and tag abundances in matrix form, usually from cellular barcoding experiments, integration site retrieval analyses, or similar technologies.

Sickle is a tool that trims reads based on quality and length thresholds. It uses sliding windows to detect low-quality bases at the 3'-end and high-quality bases at the 5'-end. Additionally, it discards reads based on the length threshold.

This package provides TagGD barcode demultiplexing utilities for Spatial Transcriptomics data.

This package provides a C library for parsing local and remote BigWig files.

This package aims to simplify working with genomic region / interval data by providing a common interface that lets you access a wide selection of file types and formats for handling genomic region data---all using the same syntax.

Scallop is a reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts.

Hclust2 is a handy tool for plotting heat-maps with several useful options to produce high quality figures that can be used in publications.

This package provides basic routines for estimation of gene-specific transcriptional derivatives and visualization of the resulting velocity patterns.

The package is ideal for analyzing RNA structure and chemical probing data.

This package is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analysis at multiple levels of resolution. This software package can assign both genomes and MAGs to SGBs. PhyloPhlAn can reconstruct strain-level phylogenies using clade- specific maximally informative phylogenetic markers, and can also scale to very large phylogenies comprising >17,000 microbial species.

ShoRAH is a project for the analysis of next generation sequencing data. It is designed to analyse genetically heterogeneous samples. Its tools provide error correction, haplotype reconstruction and estimation of the frequency of the different genetic variants present in a mixed sample.

MoFax is a Python package for transcription factor motif analysis. It provides convenience functions to load and visualize factor models trained with MOFA+ in Python.

Forester is a collection of Java libraries for phylogenomics and evolutionary biology research. It includes support for reading, writing, and exporting phylogenetic trees.

This package provides an object for plotting GRanges, RleList, UCSC file formats, and ffTrack objects in multi-track panels.

The subread package contains the following tools: subread aligner, a general-purpose read aligner; subjunc aligner: detecting exon-exon junctions and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic features; exactSNP: a SNP caller that discovers SNPs by testing signals against local background noises.

This package generates a Miami plot with centered chromosome labels. The output is a ggplot2 object. Users can specify which data they want plotted on top vs. bottom, whether to display significance line(s), what colors to give chromosomes, and what points to label.

HTSJDK is an implementation of a unified Java library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing (HTS) data. There are also an number of useful utilities for manipulating HTS data.

HTSlib is a C library for reading/writing high-throughput sequencing data. It also provides the bgzip, htsfile, and tabix utilities.

This library contains the genomics components of the Bio++ sequence library. It is part of the Bio++ project.