This package provides an automated pipeline for spatial mapping of unique transcripts.

This is an R package that integrates the installation of doublet-detection methods. In addition, this tool is used for execution and benchmark of those eight mentioned methods.

This package implements the method csSAM that computes cell-specific differential expression from measured cell proportions using SAM.

Mosaicatcher counts Strand-seq reads and classifies strand states of each chromosome in each cell using a Hidden Markov Model.

This package allows building the hierarchy of domains starting from Hi-C data. Each hierarchical level is identified by a minimum value of physical insulation between neighboring domains.

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

DNA Features Viewer is a Python library to visualize DNA features, e.g. from GenBank or Gff files, or Biopython SeqRecords.

ChIPKernels is an R package for building different string kernels used for DNA Sequence analysis. A dictionary of the desired kernel must be built and this dictionary can be used for determining kernels for DNA Sequences.

PiGx is a collection of genomics pipelines. It includes the following pipelines:

• PiGx BSseq for raw fastq read data of bisulfite experiments

• PiGx RNAseq for RNAseq samples

• PiGx scRNAseq for single cell dropseq analysis

• PiGx ChIPseq for reads from ChIPseq experiments

All pipelines are easily configured with a simple sample sheet and a descriptive settings file. The result is a set of comprehensive, interactive HTML reports with interesting findings about your samples.

MOSAIK is a program for mapping second and third-generation sequencing reads to a reference genome. MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT.

This package provides a framework for the analysis and exploration of single-cell chromatin data. The Signac package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis.

Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few built-in functions and a command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk.

python-cwl-upgrader is a standalone upgrader for CWL documents from version draft-3, v1.0, and v1.1 to v1.2.

This package is a set of R functions for generating precise figures. This tool helps you to create clean markdown reports about what you just discovered with your analysis script.

This package provides a package that makes it easy to implement sankey, alluvial and sankey bump plots in ggplot2.

Biopython is a set of tools for biological computation including parsers for bioinformatics files into Python data structures; interfaces to common bioinformatics programs; a standard sequence class and tools for performing common operations on them; code to perform data classification; code for dealing with alignments; code making it easy to split up parallelizable tasks into separate processes; and more.

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.

Bio-locus is a tabix-like tool for fast querying of genome locations. Many file formats in bioinformatics contain records that start with a chromosome name and a position for a SNP, or a start-end position for indels. Bio-locus allows users to store this chr+pos or chr+pos+alt information in a database.

PyLiftover is a library for quick and easy conversion of genomic (point) coordinates between different assemblies.

Python scripts to find enrichment of GO terms. In addition, this package is used for processing the obo-formatted file from Gene Ontology website. The data structure is a directed acyclic graph that allows easy traversal from leaf to root.

ShoRAH is a project for the analysis of next generation sequencing data. It is designed to analyse genetically heterogeneous samples. Its tools provide error correction, haplotype reconstruction and estimation of the frequency of the different genetic variants present in a mixed sample.

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can be optionally compressed by gzip.

MuSiC is a deconvolution method that utilizes cross-subject scRNA-seq to estimate cell type proportions in bulk RNA-seq data.

This helper package implements the HiCMatrix class for the HiCExplorer and pyGenomeTracks packages.