F-Seq is a software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites such as transcription factor binding sites (ChIP-seq) or regions of open chromatin (DNase-seq). Output can be displayed directly in the UCSC Genome Browser.

Centrifuge is a microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. The system uses an indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes.

The Filtlong package is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.

DelayedArray based image operations.

This package is a collection of Perl, Python, and R scripts for manipulating 3C/4C/5C/Hi-C data.

MUSIC is an algorithm for identification of enriched regions at multiple scales in the read depth signals from ChIP-Seq experiments.

This tool provides a Python framework to streamline genomics operations. It offers a direct interface to Ensembl genome assemblies and annotations, while also accommodating custom genomes via FASTA/GTF inputs. The primary objective of pybio is to simplify genome management. It achieves this by providing automatic download of Ensembl genome assemblies and annotation, provides Python genomic feature search and sequence retrieval from the managed genomes, STAR indexing and mapping and more.

This package aims to bring the power and flexibility of AnnData to the R ecosystem, allowing you to effortlessly manipulate and analyze your single-cell data. This package lets you work with backed h5ad and zarr files, directly access various slots (e.g. X, obs, var), or convert the data into SingleCellExperiment and Seurat objects.

DoubletFinder identifies doublets by generating artificial doublets from existing scRNA-seq data and defining which real cells preferentially co-localize with artificial doublets in gene expression space. Other DoubletFinder package functions are used for fitting DoubletFinder to different scRNA-seq datasets. For example, ideal DoubletFinder performance in real-world contexts requires optimal pK selection and homotypic doublet proportion estimation. pK selection is achieved using pN-pK parameter sweeps and maxima identification in mean-variance-normalized bimodality coefficient distributions. Homotypic doublet proportion estimation is achieved by finding the sum of squared cell annotation frequencies.

This is a collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

PDBFixer is designed to rectify issues in Protein Data Bank files. Its intuitive interface simplifies the process of resolving problems encountered in PDB files prior to simulation tasks.

This package provides graphical user interfaces to organize and visualize Nanopore sequencing data.

Sleuth is a program for differential analysis of RNA-Seq data. It makes use of quantification uncertainty estimates obtained via Kallisto for accurate differential analysis of isoforms or genes, allows testing in the context of experiments with complex designs, and supports interactive exploratory data analysis via sleuth live.

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

Scanorama enables batch-correction and integration of heterogeneous scRNA-seq datasets, which is described in the paper "Efficient integration of heterogeneous single-cell transcriptomes using Scanorama" by Brian Hie, Bryan Bryson, and Bonnie Berger.

SCENIC (Single-cell regulatory network inference and clustering) is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

This package provides the ASCAT R package that can be used to infer tumour purity, ploidy and allele-specific copy number profiles.

This package provides extra utility functions to perform common tasks in the analysis of omics data, leveraging and enhancing features provided by Bioconductor packages.

Telomerecat is a tool for estimating the average telomere length (TL) for a paired end, whole genome sequencing (WGS) sample.

Telomerecat is adaptable, accurate and fast. The algorithm accounts for sequencing amplification artifacts, anneouploidy (common in cancer samples) and noise generated by WGS. For a high coverage WGS BAM file of around 100GB telomerecat can produce an estimate in ~1 hour.

This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides a user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels. For visualization, it can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.

SlamDunk is a fully automated tool for automated, robust, scalable and reproducible SLAMseq data analysis. Diagnostic plotting features and a MultiQC plugin will make your SLAMseq data ready for immediate QA and interpretation.

This package provides accelerated functions for the CIRI toolkit. It also provides the ccs executable to scan for circular consensus sequences.

CellTypist is an automated cell type annotation tool for scRNA-seq datasets on the basis of logistic regression classifiers optimised by the stochastic gradient descent algorithm. CellTypist allows for cell prediction using either built-in (with a current focus on immune sub-populations) or custom models, in order to assist in the accurate classification of different cell types and subtypes.