Keywords and Expertise
Use keywords to characterize workflows and forum posts, and reach out to sellers with relevant expertise
Workflow engine and language. It aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern domain specific specification language (DSL) in python style.
SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.
Pandas is a fast, powerful, flexible and easy to use open source data analysis and manipulation tool, built on top of the Python programming language.
The fundamental package for scientific computing with Python
The full Genome Analysis Toolkit (GATK) framework, v3
This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
Create Elegant Data Visualisations Using the Grammar of Graphics: A system for 'declaratively' creating graphics, based on "The Grammar of Graphics". You provide the data, tell 'ggplot2' how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details.
MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
BEDTools is an extensive suite of utilities for comparing genomic features in BED format.
Matplotlib produces publication-quality figures in a variety of hardcopy formats and interactive environments across platforms. Matplotlib can be used in Python scripts, Python/IPython shells, web application servers, and various graphical user interface toolkits.
Easily Install and Load the 'Tidyverse': The 'tidyverse' is a set of packages that work in harmony because they share common data representations and 'API' design. This package is designed to make it easy to install and load multiple 'tidyverse' packages in a single step. Learn more about the 'tidyverse' at .
Fast, accurate, memory-efficient aligner for short and long sequencing reads
A set of command line tools for manipulating high-throughput sequencing (HTS) data in formats such as SAM/BAM/CRAM and VCF. Available as a standalone program or within the GATK4 program.
Snakemake is a workflow management system that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern specification language in python style. Snakemake workflows are essentially Python scripts extended by declarative code to define rules. Rules describe how to create output files from input files.
C library and command line tools for high-throughput sequencing data formats.
A Grammar of Data Manipulation: A fast, consistent tool for working with data frame like objects, both in memory and out of memory.
An integrated solution to management and visualization of sequencing data.
Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
JavaScript Object Notation format; a lightweight, text-based format to represent tree-structured data using key-value pairs.
Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.
-------------------------------------- seaborn: statistical data visualization ======================================= [](https://pypi.org/project/seaborn/) [](https://github.com/mwaskom/seaborn/blob/master/LICENSE) [](https://doi.org/10.21105/joss.03021) [](https://github.com/mwaskom/seaborn/actions) [](https://codecov.io/gh/mwaskom/seaborn) Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. Documentation ------------- Online documentation is available at [seaborn.pydata.org](https://seaborn.pydata.org). The docs include a [tutorial](https://seaborn.pydata.org/tutorial.html), [example
A collection of utility functions and classes for Snakemake wrappers.
Extension of 'data.frame': Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
A flexible read trimming tool for Illumina NGS data
.. image:: https://raw.githubusercontent.com/scipy/scipy/main/doc/source/_static/logo.svg :target: https://scipy.org :width: 110 :height: 110 :align: left .. image:: https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A :target: https://numfocus.org .. image:: https://img.shields.io/pypi/dm/scipy.svg?label=Pypi%20downloads :target: https://pypi.org/project/scipy/ .. image:: https://img.shields.io/conda/dn/conda-forge/scipy.svg?label=Conda%20downloads :target: https://anaconda.org/conda-forge/scipy .. image:: https://img.shields.io/badge/stackoverflow-Ask%20questions-blue.svg :target: https://stackoverflow.com/questions/tagged/scipy .. image:: https://img.shields.io/badge/DOI-10.1038%2Fs41592--019--0686--2-blue :target: https://www.nature.com/articles/s41592-019-0686-2 SciPy (pronounced "Sigh Pie") is an open-source software for mathematics, science, and engineering. It includes modules for statistics, optimization, integration, li
Pairwise aligner for genomic and spliced nucleotide sequences
Tidy Messy Data: Tools to help to create tidy data, where each column is a variable, each row is an observation, and each cell contains a single value. 'tidyr' contains tools for changing the shape (pivoting) and hierarchy (nesting and 'unnesting') of a dataset, turning deeply nested lists into rectangular data frames ('rectangling'), and extracting values out of string columns. It also includes tools for working with missing values (both implicit and explicit).
A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.
FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.
R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.
pysam - a python module for reading, manipulating and writing genomic data sets. pysam is a lightweight wrapper of the htslib C-API and provides facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the samtools and bcftools packages. The module supports compression and random access through indexing. This module provides a low-level wrapper around the htslib C-API as using cython and a high-level API for convenient access to the data within standard genomic file formats. See: http://www.htslib.org https://github.com/pysam-developers/pysam http://pysam.readthedocs.org/en/stable
A tool that finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
The MIT License (MIT) ===================== Copyright (c) 2016 Marcel Hellkamp Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT O
Simple, Consistent Wrappers for Common String Operations: A consistent, simple and easy to use set of wrappers around the fantastic 'stringi' package. All function and argument names (and positions) are consistent, all functions deal with "NA"'s and zero length vectors in the same way, and the output from one function is easy to feed into the input of another.
One or more molecular sequences, possibly with associated annotation.|This concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records. It should not normally be used for derivatives such as sequence alignments, motifs or profiles.
Utils ===== .. image:: https://travis-ci.org/haaksmash/pyutils.svg?branch=master :target: https://travis-ci.org/haaksmash/pyutils Sometimes you write a function over and over again; sometimes you look up at the ceiling and ask "why, Guido, why isn't this included in the standard library?" Well, we perhaps can't answer that question. But we can collect those functions into a centralized place! Provided things +++++++++++++++ Utils is broken up into broad swathes of functionality, to ease the task of remembering where exactly something lives. enum ---- Python doesn't have a built-in way to define an enum, so this module provides (what I think) is a pretty clean way to go about them. .. code-block:: python from utils import enum class Colors(enum.Enum): RED = 0 GREEN = 1 # Defining an Enum class allows you to specify a few # things about the way it's going to behave. class Options: frozen = True # can't change attributes stric
MATLAB program for protein quantitation by iTRAQ.
User-friendly tools for the normalization and visualization of deep-sequencing data.
featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.
Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.
Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing).
Bowtie is an ultrafast, memory-efficient short read aligner.
A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides.
Tools for dealing with SAM, BAM and CRAM files