This package is a library to enable flexible and scalable operations on genomic interval dataframes in Python. Bioframe enables access to a rich set of dataframe operations. Working in Python enables rapid visualization and iteration of genomic analyses. The philosophy underlying bioframe is to enable flexible operations. Instead of creating a function for every possible use-case, we encourage users to compose functions to achieve their goals.

This package provides a C library for parsing local and remote BigWig files.

This package provides a method to detect and enable removal of doublets from single-cell RNA-sequencing.

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 provides different statistical methods to extract biological activities from omics data within a unified framework.

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

TopHat is a fast splice junction mapper for nucleotide sequence reads produced by the RNA-Seq method. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

This package is a collection of Perl, Python, and R scripts for manipulating 3C/4C/5C/Hi-C data.

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.

MAFFT offers a range of multiple alignment methods for nucleotide and protein sequences. For instance, it offers L-INS-i (accurate; for alignment of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000 sequences).

Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current parallelised functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth.

Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments.

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.

Isolator analyzes RNA-Seq experiments. Isolator has a particular focus on producing stable, consistent estimates. It implements a full hierarchical Bayesian model of an entire RNA-Seq experiment. It saves all the samples generated by the sampler, which can be processed to compute posterior probabilities for arbitrarily complex questions, far beyond the confines of pairwise tests. It aggressively corrects for technical effects, such as random priming bias, GC-bias, 3' bias, and fragmentation effects. Compared to other MCMC approaches, it is exceedingly efficient, though generally slower than modern maximum likelihood approaches.

MUSCLE aims to be a fast and accurate multiple sequence alignment program for nucleotide and protein sequences.

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 provides a framework to process and analyze data from high-throughput sequencing (HTS) assays

This package provides accelerated functions for the CIRI toolkit. It also provides the ccs executable to scan for circular consensus sequences.

Millefy is a tool for visualizing read coverage of scRNA-seq(single-cell RNA sequencing) datasets in genomic contexts. By dynamically and automatically reorder single cells based on locus-specific pseudo time, Millefy highlights cell-to-cell heterogeneity in read coverage of scRNA-seq data.

WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible.

WebLogo can create output in several common graphics' formats, including the bitmap formats GIF and PNG, suitable for on-screen display, and the vector formats EPS and PDF, more suitable for printing, publication, and further editing. Additional graphics options include bitmap resolution, titles, optional axis, and axis labels, antialiasing, error bars, and alternative symbol formats.

A sequence logo is a graphical representation of an amino acid or nucleic acid multiple sequence alignment. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. The width of the stack is proportional to the fraction of valid symbols in that position.

This package provides helper functions to detect cross-hybridization on Illumina DNAm arrays.

Kraken is a taxonomic sequence classifier that assigns taxonomic labels to DNA sequences. Kraken examines the k-mers within a query sequence and uses the information within those k-mers to query a database. That database maps k-mers to the lowest common ancestor (LCA) of all genomes known to contain a given k-mer.

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.

SlamDunk is a fully automated tool for automated, robust, scalable and reproducible SLAMseq data analysis. Diagnostic plotting features and a MultiQC plugin will make your SLAMseq data ready for immediate QA and interpretation.