gffcompare is a tool that can:

1. compare and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie);

2. collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g. resulted from assembly of different samples);

3. classify transcripts from one or multiple GTF/GFF3 files as they relate to reference transcripts provided in a annotation file (also in GTF/GFF3 format).

CodingQuarry is a highly accurate, self-training GHMM fungal gene predictor designed to work with assembled, aligned RNA-seq transcripts.

EpiScanpy is a toolkit to analyse single-cell open chromatin (scATAC-seq) and single-cell DNA methylation (for example scBS-seq) data. EpiScanpy is the epigenomic extension of the very popular scRNA-seq analysis tool Scanpy (Genome Biology, 2018).

Samtools implements various utilities for post-processing nucleotide sequence alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer.

MultiQC is a tool to aggregate bioinformatics results across many samples into a single report. It contains modules for a large number of common bioinformatics tools.

BSeq-sc is a bioinformatics analysis pipeline that leverages single-cell sequencing data to estimate cell type proportion and cell type-specific gene expression differences from RNA-seq data from bulk tissue samples. This is a companion package to the publication "A single-cell transcriptomic map of the human and mouse pancreas reveals inter- and intra-cell population structure." Baron et al. Cell Systems (2016) https://www.ncbi.nlm.nih.gov/pubmed/27667365.

hdWGCNA is an R package for performing weighted gene co-expression network analysis in high dimensional -omics such as single-cell RNA-seq or spatial transcriptomics.

MinCED is a program to find Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in DNA sequences. It can be used for unassembled metagenomic reads, but is mainly designed for full genomes and assembled metagenomic sequence.

This package offers Cython bindings and a Python interface for Prodigal. Prodigal is an ORF finder designed for both genomes and metagenomes.

The NCBI-VDB library implements a highly compressed columnar data warehousing engine that is most often used to store genetic information. Databases are stored in a portable image within the file system, and can be accessed/downloaded on demand across HTTP.

HTSlib is a C library for reading/writing high-throughput sequencing data. It also provides the bgzip, htsfile, and tabix utilities.

t-Stochastic Neighborhood Embedding (t-SNE) is a highly successful method for dimensionality reduction and visualization of high dimensional datasets. A popular implementation of t-SNE uses the Barnes-Hut algorithm to approximate the gradient at each iteration of gradient descent. This package is a Cython wrapper for FIt-SNE.

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

This package performs a fast Wilcoxon rank sum test and auROC analysis.

FAN-C provides a pipeline for analysing Hi-C data starting at mapped paired-end sequencing reads.

PAML (for Phylogentic Analysis by Maximum Likelihood) contains a few programs for model fitting and phylogenetic tree reconstruction using nucleotide or amino-acid sequence data.

This package provides a client for the OmniPath web service and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation nichenetr.

This package provides an implementation of the BITS (Binary Interval Search) algorithm, an approach to interval set intersection. It is especially suited for the comparison of diverse genomic datasets and the exploration of large datasets of genome intervals (e.g. genes, sequence alignments).

LIANA provides a number of methods and resource for ligand-receptor interaction inference from scRNA-seq data.

This package is a Python-based command line interface for processing .bam files with mitochondrial reads and generating high-quality heteroplasmy estimation from sequencing data. The mgatk package places a special emphasis on mitochondrial genotypes generated from single-cell genomics data, primarily mtscATAC-seq, but is generally applicable across other assays.

IMP's broad goal is to contribute to a comprehensive structural characterization of biomolecules ranging in size and complexity from small peptides to large macromolecular assemblies, by integrating data from diverse biochemical and biophysical experiments. IMP provides a C++ and Python toolbox for solving complex modeling problems, and a number of applications for tackling some common problems in a user-friendly way.

This package provides data for the book "Computational Genomics with R".

The SCDE package implements a set of statistical methods for analyzing single-cell RNA-seq data. SCDE fits individual error models for single-cell RNA-seq measurements. These models can then be used for assessment of differential expression between groups of cells, as well as other types of analysis. The SCDE package also contains the pagoda framework which applies pathway and gene set overdispersion analysis to identify aspects of transcriptional heterogeneity among single cells.

This package is a Python wrapper for Aaron Quinlan's BEDtools programs, which are widely used for genomic interval manipulation or "genome algebra". pybedtools extends BEDTools by offering feature-level manipulations from with Python.