This package is used for cell type identification in spatial transcriptomics. It also handles cell type-specific differential expression.

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.

This package is intended to help users to efficiently analyze genomic data resulting from various experiments.

CD-HIT is a program for clustering and comparing protein or nucleotide sequences. CD-HIT is designed to be fast and handle extremely large databases.

Scallop is a reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts.

A tiny C library for managing SOM (Self-Organizing Maps) neural networks.

This is a collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

BioJava is a project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.

This package provides the core libraries.

This R package provides additional capabilities and speed for GenomicRanges operations.

Drop-seq is a technology to enable biologists to analyze RNA expression genome-wide in thousands of individual cells at once. This package provides tools to perform Drop-seq analyses.

This library implements an efficient loopless multiset combination generation algorithm which is (approximately) described in "Loopless algorithms for generating permutations, combinations, and other combinatorial configurations.", G. Ehrlich - Journal of the ACM (JACM), 1973. (Algorithm 7.)

PySnpTools is a library for reading and manipulating genetic data. It can, for example, efficiently read whole PLINK *.bed/bim/fam files or parts of those files. It can also efficiently manipulate ranges of integers using set operators such as union, intersection, and difference.

This package is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analysis at multiple levels of resolution. This software package can assign both genomes and MAGs to SGBs. PhyloPhlAn can reconstruct strain-level phylogenies using clade- specific maximally informative phylogenetic markers, and can also scale to very large phylogenies comprising >17,000 microbial species.

CD-HIT is a program for clustering and comparing protein or nucleotide sequences. CD-HIT is designed to be fast and handle extremely large databases.

Bamnostic is a pure Python Binary Alignment Map (BAM) file parser and random access tool.

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 conducts batch effects removal from a taxa read count table by a conditional quantile regression method. The distributional attributes of microbiome data - zero-inflation and over-dispersion, are simultaneously considered.

This package generates a Miami plot with centered chromosome labels. The output is a ggplot2 object. Users can specify which data they want plotted on top vs. bottom, whether to display significance line(s), what colors to give chromosomes, and what points to label.

MACS is an implementation of a ChIP-Seq analysis algorithm for identifying transcript factor binding sites named Model-based Analysis of ChIP-Seq (MACS). MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions and it improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation.

This package provides Python bindings to the bwa mem aligner.

Several studies focus on the inference of developmental and response trajectories from single cell RNA-Seq (scRNA-Seq) data. A number of computational methods, often referred to as pseudo-time ordering, have been developed for this task. CRISPR has also been used to reconstruct lineage trees by inserting random mutations. The tbsp package implements an alternative method to detect significant, cell type specific sequence mutations from scRNA-Seq data.

Maxent is a stand-alone Java application for modelling species geographic distributions.

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.

Splicekit is a modular platform for splicing analysis from short-read RNA-seq datasets. The platform also integrates pybio for genomic operations and scanRBP for RNA-protein binding studies. The whole analysis is self-contained (one single directory) and the platform is written in Python, in a modular way.