This package provides data structures, algorithms and educational resources for bioinformatics.

PRANK is a probabilistic multiple sequence alignment program for DNA, codon and amino-acid sequences. It is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. In addition, PRANK borrows ideas from maximum likelihood methods used in phylogenetics and correctly takes into account the evolutionary distances between sequences. Lastly, PRANK allows for defining a potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.

This package implements a bioinformatics algorithm for demultiplexing multiplexed single cell datasets. It is built on a statistical model of tag read counts derived from the physical mechanism of tag cross-contamination.

This package lets you read and write the PLINK BED format, simply and efficiently.

This package contains data used by pagoda2. The data within this package are the 3000 bone marrow cells used for vignettes.

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

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.

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

ParDRe is a parallel tool to remove duplicate genetic sequence reads. Duplicate reads can be seen as identical or nearly identical sequences with some mismatches. This tool lets users avoid the analysis of unnecessary reads, reducing the time of subsequent procedures with the dataset (e.g. assemblies, mappings, etc.). The tool is implemented with MPI in order to exploit the parallel capabilities of multicore clusters. It is faster than multithreaded counterparts (end of 2015) for the same number of cores and, thanks to the message-passing technology, it can be executed on clusters.

twobitreader is a Python library for reading .2bit files as used by the UCSC genome browser.

Skewer implements the bit-masked k-difference matching algorithm dedicated to the task of adapter trimming and it is specially designed for processing next-generation sequencing (NGS) paired-end sequences.

This package provides a a transcriptomic-based framework to dissect cell communication in a global manner. It integrates an original expert-curated database of ligand-receptor interactions taking into account multiple subunits expression. Based on transcriptomic profiles (gene expression), this package computes communication scores between cells and provides several visualization modes that can be helpful to dig into cell-cell interaction mechanism and extend biological knowledge.

Pegasusio is a Python package for reading or writing single-cell genomics data.

NanoSV is a software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies’ MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers.

This is a simple "libraryfication" of the GFF/GTF parsing code that is used in the Cufflinks codebase. The goal of this library is to provide this functionality without the necessity of drawing in a heavy-weight dependency like SeqAn.

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

The gdc-client provides several convenience functions over the GDC API which provides general download/upload via HTTPS.

This package provides an implementation of chunked, compressed, N-dimensional arrays for R, Zarr specification version 2 (2024) <doi:10.5281/zenodo.11320255>.

This package is a rasterization preprocessing framework that aggregates cellular information into spatial pixels to reduce resource requirements for spatial omics data analysis. SEraster reduces the number of points in spatial omics datasets for downstream analysis through a process of rasterization where single cells gene expression or cell-type labels are aggregated into equally sized pixels based on a user-defined resolution. SEraster can be incorporated with other packages to conduct downstream analyses for spatial omics datasets, such as detecting spatially variable genes.

Bioinformaticians often have to convert sequence files between formats and do little manipulations on them, and it's not worth writing scripts for that. Seqmagick is a utility to expose the file format conversion in BioPython in a convenient way. Instead of having a big mess of scripts, there is one that takes arguments.

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. It is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.

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.

PyEGA3 is a tool for viewing and downloading files from authorized EGA datasets. It uses the EGA data API and has several key features:

• Files are transferred over secure https connections and received unencrypted, so no need for decryption after download.

• Downloads resume from where they left off in the event that the connection is interrupted.

• Supports file segmenting and parallelized download of segments, improving overall performance.

• After download completes, file integrity is verified using checksums.

• Implements the GA4GH-compliant htsget protocol for download of genomic ranges for data files with accompanying index files.

This package provides an assortment of R functions that is suitable for all types of microbial diversity analyses.