This package provides a computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data.

This is a package for the discovery of communities in Pore-C concatemers.

BitMapperBS is memory-efficient aligner that is designed for whole-genome bisulfite sequencing (WGBS) reads from directional protocol.

This package provides a Python package for reading raw fcs files

The porechop package is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity. Porechop also supports demultiplexing of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.

R-scape discovers RNA secondary structure consensus elements. These elements include riboswitches and ribozymes. It utilizes probabilistic modeling of sequence alignments, explicitly considering folding dependencies. The tool enables the de novo search for new structural elements and facilitates comparative analysis of known RNA families.

Zarr backend for DelayedArray objects.

VSEARCH supports DNA sequence searching, clustering, chimera detection, dereplication, pairwise alignment, shuffling, subsampling, sorting and masking. The tool takes advantage of parallelism in the form of SIMD vectorization as well as multiple threads to perform accurate alignments at high speed. VSEARCH uses an optimal global aligner (full dynamic programming Needleman-Wunsch).

QTLtools is a tool set for molecular QTL discovery and analysis. It allows going from the raw genetic sequence data to collection of molecular Quantitative Trait Loci (QTLs) in few easy-to-perform steps.

This is an R package providing additional capabilities and speed for GenomicRanges operations.

SeqAn is a C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. It contains algorithms and data structures for string representation and their manipulation, online and indexed string search, efficient I/O of bioinformatics file formats, sequence alignment, and more.

VoltRon is a novel spatial omic analysis toolbox for multi-omics integration using spatial image registration. VoltRon is capable of analyzing multiple types and modalities of spatially-aware datasets. VoltRon visualizes and analyzes regions of interests (ROIs), spots, cells and even molecules.

This package lets you perform unsupervised clustering of amplicon sequencing data in microbiome studies with the Dirichlet-tree Multinomial Mixtures.

This tool detects batch effects in high-dimensional data based on chi^2-test.

BamTools provides both a C++ API and a command-line toolkit for handling BAM files.

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.

This package implements bindings for h5 files that are compatible with Bioconductor S4 data structures, namely the DataFrame and DelayedArray. This allows HDF5-backed data to be easily used as data frames with arbitrary sets of columns.

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

NGS is a domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously.

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.

This package provides a collection of useful functions for working with DNA methylation micro-array data.

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

Azimuth utilizes an annotated reference dataset. It automates the processing, analysis, and interpretation. This applies specifically to new single-cell RNA-seq or ATAC-seq experiments. Azimuth leverages a reference-based mapping pipeline that inputs accounts matrix and performs normalization, visualization, cell annotation, and differential expression.

This package provides Shiny apps for interactive exploration of single-cell data.