Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.

This is an R package which interfaces with the OME Bio-Formats Java library to allow reading of proprietary microscopy image data and metadata.

This package provides an implementation of run length arithmetic in Python using Cython. This is a support library for the pyranges stack.

This package contains functions to extract information from Oxford Nanopore sequencing data and alignments.

This package contains a few simple math function for other Oxford Nanopore processing scripts.

MetaMaps is tool specifically developed for the analysis of long-read (PacBio/Oxford Nanopore) metagenomic datasets.

tsdate is a scalable method for estimating the age of ancestral nodes in a tree sequence. The method uses a coalescent prior and updates node times on the basis of the number of mutations along each edge of the tree sequence (i.e. using the "molecular clock").

This package is used to apply filtering on raw VCF calls generated using CaVEMan.

This package provides the C library for the BGEN format (specifications 1.2 and 1.3).

hypothesis-vcf is designed to generate VCF files that conform to the VCF specification (version 4.3). It generates VCFs that are syntactically valid, but which don't have meaningful semantics.

This package provides a Cython helper library for pyranges for finding nearest intervals in linear time at C speed.

Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm, which is used to generate consensus sequences. It supports three alignment modes: local (Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment (overlap), and three gap modes: linear, affine and convex (piecewise affine).

This package provides a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). It uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. It further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.

Biosoup is a C++ collection of header-only data structures used for storage and logging in bioinformatics tools.

The NCL is a C++ library for interpreting data files created according to the NEXUS file format used in phylogenetic systematics and molecular evolution.

Succinct tree sequences are an efficient way of representing the genetic history - often technically referred to as an Ancestral Recombination Graph or ARG - of a set of DNA sequences.

The tree sequence format is output by a number of external software libraries and programs (such as msprime, SLiM, fwdpp, and tsinfer) that either simulate or infer the evolutionary ancestry of genetic sequences. This library provides the underlying functionality that such software uses to load, examine, and manipulate ARGs in tree sequence format, including efficientaccess to the correlated sequence of trees along a genome and general methods to calculate genetic statistics.

SHARC is a pipeline for somatic SV calling and filtering from tumor-only Nanopore sequencing data. It performs mapping, SV calling, SV filtering, random forest classification, blacklist filtering and SV prioritization, followed by automated primer design for PCR amplicons of 80-120 bp that are useful to track cancer ctDNA molecules in liquid biopsies.

This package provides a fast implementation of Fisher's exact test for Python.

This package provides a new way of computing bootstrap supports in large phylogenies.

POLEGON works with inferred ARG to re-calibrate the branch length, without the usage of any prior.

The io_lib from the Staden package is a library of file reading and writing code to provide a general purpose trace file (and Experiment File) reading interface. It supports various DNA sequence read formats, in particular SCF, ABI, ALF, CTF, ZTR, SFF and SRF.

PyRanges is a Python library specifically designed for efficient and intuitive manipulation of genomics data, particularly genomic intervals (like genes, genomic features, or reads). The library is optimized for fast querying and manipulation of genomic annotations.

This package contains a set of common Perl utilities for generating consistent Vcf headers. It primarily exists to prevent code duplication between some other projects.

IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data such as:

• Recombination model probability distribution

• Hypermutation model

• Best candidates recombination scenarios

• Generation probabilities of sequences (even hypermutated)

Its heavily object oriented and modular style was designed to ensure long term support and evolvability for new tasks in assessing TCR and BCR receptors features using modern parallel architectures.