This package provides a convenient interface to minimap2, a fast and accurate C program to align genomic and transcribe nucleotide sequences.

This is a C++ wrapper around the Tabix project which abstracts some of the details of opening and jumping in tabix-indexed files.

BBKNN is a batch effect removal tool that can be directly used in the Scanpy workflow. It serves as an alternative to scanpy.api.pp.neighbors(), with both functions creating a neighbour graph for subsequent use in clustering, pseudotime and UMAP visualisation. If technical artifacts are present in the data, they will make it challenging to link corresponding cell types across different batches. BBKNN actively combats this effect by splitting your data into batches and finding a smaller number of neighbours for each cell within each of the groups. This helps create connections between analogous cells in different batches without altering the counts or PCA space.

PLINK is a whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.

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.

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.

Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. Pseudoalignment of reads preserves the key information needed for quantification, and kallisto is therefore not only fast, but also as accurate as existing quantification tools.

The ZarrArray package leverages the Rarr package to bring Zarr datasets in R as DelayedArray objects. The main class in the package is the ZarrArray class. A ZarrArray object is an array-like object that represents a Zarr dataset in R. ZarrArray objects are DelayedArray derivatives and therefore support all operations (delayed or block-processed) supported by DelayedArray objects.

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

This package detects naive associations between omics features and metadata in cross-sectional data-sets using non-parametric tests. In a second step, confounding effects between metadata associated to the same omics feature are detected and labeled using nested post-hoc model comparison tests. The generated output can be graphically summarized using the built-in plotting function.

This package implements methods to project single-cell RNA-seq data onto a reference atlas, enabling interpretation of unknown cell transcriptomic states in the the context of known, reference states.

dRep is a Python program for rapidly comparing large numbers of genomes. dRep can also "de-replicate" a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set.

CENTIPEDE applies a hierarchical Bayesian mixture model to infer regions of the genome that are bound by particular transcription factors. It starts by identifying a set of candidate binding sites, and then aims to classify the sites according to whether each site is bound or not bound by a transcription factor. CENTIPEDE is an unsupervised learning algorithm that discriminates between two different types of motif instances using as much relevant information as possible.

This framework facilitates the execution of differential junction usage (DJU) methods. Additionally, it enables the integration of results from multiple DJU methods.

LoFreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.

The metacells package implements the improved metacell algorithm for single-cell RNA sequencing (scRNA-seq) data analysis within the scipy framework, and projection algorithm based on it. The original metacell algorithm was implemented in R. The Python package contains various algorithmic improvements and is scalable for larger data sets (millions of cells).

PyGAD is a Python library for building the genetic algorithm and optimizing machine learning algorithms. It supports Keras and PyTorch, and it can optimize both single-objective and multi-objective problems.

SnapTools can operate on snap files the following types of operations:

• index the reference genome before alignment;

• align reads to the corresponding reference genome;

• pre-process by convert pair-end reads into fragments, checking the mapping quality score, alignment and filtration;

• create the cell-by-bin matrix.

RSeQC provides a number of modules that can comprehensively evaluate high throughput sequence data, especially RNA-seq data. Some basic modules inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, etc.

GNU Bison is a general-purpose parser generator. It can build a deterministic or generalized LR parser from an annotated, context-free grammar. It is versatile enough to have many applications, from parsers for simple tools through complex programming languages.

Bison also provides an implementation of yacc, as specified by POSIX.

transmission-remote-gtk is a GTK client for remote management of the Transmission BitTorrent client, using its HTTP RPC protocol.

qBittorrent is a BitTorrent client programmed in C++/Qt that uses libtorrent (sometimes called libtorrent-rasterbar) by Arvid Norberg.

It aims to be a good alternative to all other BitTorrent clients out there. qBittorrent is fast, stable and provides unicode support as well as many features.

Transmission is a BitTorrent client that comes with graphical, textual, and Web user interfaces. Transmission also has a daemon for unattended operations. It supports local peer discovery, full encryption, DHT, µTP, PEX and Magnet Links.

rTorrent is a BitTorrent client with an ncurses interface. It supports full encryption, DHT, PEX, and Magnet Links. It can also be controlled via XML-RPC over SCGI.