This package provides an automated pipeline for spatial mapping of unique transcripts.

Taxtastic is software written in python used to build and maintain reference packages i.e. collections of reference trees, reference alignments, profiles, and associated taxonomic information.

This helper package implements the HiCMatrix class for the HiCExplorer and pyGenomeTracks packages.

This package provides a GFF/GTF file parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.

PhyML is a software package that uses modern statistical approaches to analyse alignments of nucleotide or amino acid sequences in a phylogenetic framework. The main tool in this package builds phylogenies under the maximum likelihood criterion. It implements a large number of substitution models coupled with efficient options to search the space of phylogenetic tree topologies. codePhyREX fits the spatial-Lambda-Fleming-Viot model to geo-referenced genetic data. This model is similar to the structured coalescent but assumes that individuals are distributed along a spatial continuum rather than discrete demes. PhyREX can be used to estimate population densities and rates of dispersal. Its output can be processed by treeannotator (from the BEAST package) as well as SPREAD.

Sailfish is a tool for genomic transcript quantification from RNA-seq data. It requires a set of target transcripts (either from a reference or de-novo assembly) to quantify. All you need to run sailfish is a fasta file containing your reference transcripts and a (set of) fasta/fastq file(s) containing your reads.

The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process.

Megahit is a fast and memory-efficient NGS assembler. It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single-cell assembly.

Salad is a schema language for describing JSON or YAML structured linked data documents. Salad schema describes rules for preprocessing, structural validation, and hyperlink checking for documents described by a Salad schema. Salad supports rich data modeling with inheritance, template specialization, object identifiers, object references, documentation generation, code generation, and transformation to RDF. Salad provides a bridge between document and record oriented data modeling and the Semantic Web.

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

This package facilitates the analysis of single-cell RNA-seq UMI matrices. It does this by computing partitions of a cell similarity graph into small homogeneous groups of cells, which are defined as metacells (MCs). The derived MCs are then used for building different representations of the data, allowing matrix or 2D graph visualization forming a basis for analysis of cell types, subtypes, transcriptional gradients,cell-cycle variation, gene modules and their regulatory models and more.

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

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. Jellyfish is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in a binary format, which can be translated into a human-readable text format using the jellyfish dump command, or queried for specific k-mers with jellyfish query.

This package provides a toolbox to process, analyze and visualize spatial single-cell expression data.

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.

The Maxprobes package collects cross-reactive probes of Illumina methylation array 450K and EPIC/850K.

This package performs a fast Wilcoxon rank sum test and auROC analysis.

Mash is a fast sequence distance estimator that uses the MinHash algorithm and is designed to work with genomes and metagenomes in the form of assemblies or reads.

Bio-locus is a tabix-like tool for fast querying of genome locations. Many file formats in bioinformatics contain records that start with a chromosome name and a position for a SNP, or a start-end position for indels. Bio-locus allows users to store this chr+pos or chr+pos+alt information in a database.

This is a package providing efficient operations for single cell ATAC-seq fragments and RNA counts matrices. It is interoperable with standard file formats, and introduces efficient bit-packed formats that allow large storage savings and increased read speeds.

This package provides tools for dealing with Unique Molecular Identifiers (UMIs) and Random Molecular Tags (RMTs) in genetic sequences. There are six tools: the extract and whitelist commands are used to prepare a fastq containing UMIs +/- cell barcodes for alignment. The remaining commands, group, dedup, and count/count_tab, are used to identify PCR duplicates using the UMIs and perform different levels of analysis depending on the needs of the user.

This package analyses the Oxford Nanopore sequencing data at signal-level. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs (Single nucleotide polymorphisms) and indels with respect to a reference genome and more.

python-cwl-utils provides python utilities and autogenerated classes for loading and parsing CWL v1.0, CWL v1.1, and CWL v1.2 documents.

Circus is an R package for annotation, analysis and visualization of circRNA data. Users can annotate their circRNA candidates with host genes, gene features they are spliced from, and discriminate between known and yet unknown splice junctions. Circular-to-linear ratios of circRNAs can be calculated, and a number of descriptive plots easily generated.