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preseq

aimed at predicting and estimating the complexity of a genomic sequencing library

Versions:2.0
License:GPLv2
Categories:bioinformatics
prodigal

Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program.

Versions:2.6.2; 2.6.3
License:GPL3
Categories:Bioinformatics gene genefinding genetics
proj

PROJ is a generic coordinate transformation software that transforms geospatial coordinates from one coordinate reference system (CRS) to another.

Versions:6.1.0; 6.2.0
License:MIT License
Categories:data sciencel, graphics
proj4

Cartographic Projections Library

Versions:4.9.2
License:MIT
Categories:GIS, library
provean

Protein Variation Effect Analyzer

Versions:1.1.5
License:GPLv2
Categories:bioinformatics
psycopg2

a swiss-army knife of tools for a wide-range of genomics analysis tasks.

Versions:2.6.1
License:GPLv2
Categories:bioinformatics
pycogent

PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: controlling third-party applications; devising workflows; querying databases; conducting novel probabilistic analyses of biological sequence evolution; and generating publication quality graphics.

Versions:1.9
License:GPLv2
Categories:
pyinstaller

PyInstaller bundles a Python application and all its dependencies into a single package. The user can run the packaged app without installing a Python interpreter or any modules.

Versions:3.2
License:Python, Application, Utility
Categories:
pymvpa2

PyMVPA stands for MultiVariate Pattern Analysis (MVPA) in Python.

Versions:2.4.1-1
License:MIT License https://opensource.org/licenses/mit-license.php
Categories:statistics
pyqi

pyqi (canonically pronounced pie chee) is a Python framework designed to support wrapping general commands in multiple types of interfaces, including at the command line, HTML, and API levels.

Versions:0.3.2
License:BSD
Categories:
pyrad

Assembly and analysis of RADseq data sets

Versions:3.0.66; 3.0.5
License:GNU GPL v3
Categories:Assembly, bioinformatics
python-anaconda-arc-connect

Python distribution for scientific computing, including accelerated commercial versions of several Python packages. Contains both Python 3 and Python2.

Versions:latest; 201704
License:Academic Cluster License, https://docs.continuum.io/anaconda/eula
Categories:IPython, Jupyter, Programming, astropy, biopython, matplotlib, numpy, python, scipy, scripting
python-anaconda2

Python 2 distribution for scientific computing, including accelerated commercial versions of several Python packages.

Versions:latest-without-openmpi; 201607; latest; 201704
License:Academic Cluster License, https://docs.continuum.io/anaconda/eula
Categories:IPython, Jupyter, Programming, astropy, biopython, matplotlib, numpy, python, scipy, scripting
python-anaconda2-base

Python 2 distribution for scientific computing, including accelerated commercial versions of several Python packages.

Versions:latest
License:Academic Cluster License, https://docs.continuum.io/anaconda/eula
Categories:IPython, Jupyter, Programming, astropy, biopython, matplotlib, numpy, python, scipy, scripting
python-anaconda3

Python 3 distribution for scientific computing, including accelerated commercial versions of several Python packages.

Versions:201607; latest; latest-3.6; 201704
License:Academic Cluster License, https://docs.continuum.io/anaconda/eula
Categories:IPython, Jupyter, Programming, astropy, biopython, matplotlib, numpy, python, scipy, scripting
python-anaconda3-base

Python 3 distribution for scientific computing, including accelerated commercial versions of several Python packages.

Versions:latest
License:Academic Cluster License, https://docs.continuum.io/anaconda/eula
Categories:IPython, Jupyter, Programming, astropy, biopython, matplotlib, numpy, python, scipy, scripting
python-antismash

Multipurpose programming language

Versions:2.0
License:GPLv2
Categories:bioinformatics
python-dev

Python is a general purpose programming language

Versions:3.5.2
License:https://opensource.org/licenses/Python-2.0
Categories:Programming, language
python-epd

Enthought Python Distribution

Versions:7.6-1
License:GPL
Categories:Programming, library, matplotlib, numpy, python, scipy
Q-chem

[SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] Q-Chem is a comprehensive ab initio quantum chemistry package for accurate predictions of molecular structures, reactivities, and vibrational, electronic and NMR spectra.

Versions:experimental with 4.4/intel; 3.2; 4.4 with OpenMPI/intel; 4.4 with serial/intel
License:See https://www.q-chem.com/qchem-website/about-qchem4.html for how to obtain a Q-chem developer license.
Categories:DFT, Hartree-Fock, Molecular structure, Quantum Chemistry, vibrational spectroscopy.
QC3

A quality control tool designed for DNA sequencing data

Versions:1.33
License:GPLv2
Categories:bioinformatics
qcli

Utilities for parsing command line options and arguments

Versions:0.1.1
License:GPL
Categories:
qiime

QIIME. (canonically pronounced chime) stands for Quantitative Insights Into Microbial Ecology.

Versions:2.0.6
License:GPLv2
Categories:bioinformatics
QoRTs

package for management of RNS-Seq datasets

Versions:1.3.6
License:Public Domain
Categories:Genomics, bioinformatics
qpdf

QPDF is a command-line program that does structural, content-preserving transformations on PDF files.

Versions:20190703
License:Apache v2
Categories:Text Processing
quast

QUAST evaluates genome assemblies.

Versions:4.5; 4.3
License:GPL2
Categories:bioinformatics assemblies
R

R environment for statistical computing and graphics

Versions:3.5.0; 3.5.1; 3.4.1; 3.6.1; 3.3.0; 3.3.2; 3.4.2; 3.3.3
License:GPL, https://www.r-project.org/Licenses/
Categories:big data, data science, graphics, statistics
r-biomed-libs

R libraries for bioinformatics, genomics, and sequencing.

Versions:3.5.0; 3.3; 3.3.2
License:GPLv2
Categories:bioinformatics
r8s

This package implements several methods to infer divergence times on a molecular

Versions:1.81
License:GPL
Categories:bioinformatics
raisd

RAiSD: Software for selective sweep detection.

Versions:1.3
License:???
Categories:bioinformatics
rate4site

Rate4Site is a program for detecting conserved amino-acid sites

Versions:2.01
License:GPLv2
Categories:bioinformatics
raxml

RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It can also be used for post-analyses of sets of phylogenetic trees, analyses of alignments and, evolutionary placement of short reads.

Versions:8.2.8; 7.2.8
License:GNU GPL v3
Categories:Phylogentics, bioinformatics
rclone

rclone is a command line program to sync files and directories to and from many cloud storage providers

Versions:1.40
License:MIT License
Categories:File Transfer, Utilities
rdptools

The RDPTools project includes the modules from the RDP (Classifier, Clustering, SequenceMatch, ProbeMatch, InitialProcessing, FrameBot, ReadSeq, Xander) and all their dependencies.

Versions:1.0.0
License:https://github.com/rdpstaff/RDPTools
Categories:Application, Biostatistics, Java
repeatmasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).

Versions:open-4.0.7; 4.0.6
License:OSL-2.1
Categories:DNA sequence, DNA sequence masking., DNA sequence scanning
RepeatModeler

RepeatModeler is a de-novo repeat family identification and modeling package.

Versions:open-1.0.8
License:OSL-2.1
Categories:DNA sequence, DNA sequence masking., DNA sequence scanning
RepeatTools

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).

Versions:open-4.0.7
License:OSL-2.1
Categories:DNA sequence, DNA sequence masking., DNA sequence scanning
reportlab

The ReportLab Toolkit. An Open Source Python library for generating PDFs and graphics.

Versions:3.2.0
License:GPLv2
Categories:bioinformatics
rfmix

RFMIX – Local Ancestry and Admixture Inference Version 2

Versions:2.0
License:GPLv2
Categories:bioinformatics
Rgeospatial

R environment for geospatial statistics

Versions:3.5.0
License:GPL, https://www.r-project.org/Licenses/
Categories:Geospatial, data science, graphics, statistics
Current page: 10
Total pages: 13
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