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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:
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: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-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-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
quast

QUAST evaluates genome assemblies.

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

R environment for statistical computing and graphics

Versions:3.4.1; 3.3.0; 3.3.2; 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:3.3; 3.3.2
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
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:4.0.6
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
Rgputools

R gputools library

Versions:R-3.3
License:GPL-3
Categories:CUDA, gpu, statistics
rmblast

RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite.

Versions:2.2.28
License:GPLv2
Categories:bioinformatics
Rmkl

R environment for statistical computing and graphics

Versions:3.3.0
License:GPL, https://www.r-project.org/Licenses/
Categories:big data, data science, graphics, statistics
Rmpi

R environment for statistical computing and graphics

Versions:3.3.0; 3.3.3
License:GPL, https://www.r-project.org/Licenses/
Categories:big data, data science, graphics, statistics
roary

Roary is a high speed stand alone pan genome pipeline

Versions:3.7.0
License:GPLv3
Categories:bioinformatics
rosetta

Rosetta is a very large software suite for macromolecular modeling.

Versions:3.7
License:GPLv2
Categories:bioinformatics
rsem

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.

Versions:1.2.31
License:GPLv3
Categories:bioinformatics
RStudio-desktop

RStudio Server IDE is a powerful and productive user interface for R.

Versions:1.1.201
License:AGPL
Categories:IDE, big data, data science, graphics, statistics
RStudio-server

RStudio Server IDE is a powerful and productive user interface for R. This is a special version of RStudio Server used by ARC Connect ( https://connect.arc-ts.umich.edu/ )

Versions:0.99.903; 1.1.201; 1.0.44
License:AGPL
Categories:ARC Connect, IDE, big data, data science, graphics, statistics, web
sage

SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. Access their combined power through a common, Python-based language or directly via interfaces or wrappers.

Versions:7.2
License:GNU GPL v3
Categories:Math, Programming
salmon

Salmon is a tool for wicked-fast transcript quantification from RNA-seq data.

Versions:0.8.2
License:GPLv3
Categories:bioinformatics
samtools

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.

Versions:0.1.19; 1.2; 1.5; 1.3.1
License:GPLv3
Categories:bioinformatics
sas

SAS statistical system software.

Versions:9.4-TS1M4; 9.4
License:Not available
Categories:Statitics, econometrics
scipy-dev

Scientific libraries for use within Python.

Versions:0.17.1
License:http://www.scipy.org/scipylib/license.html
Categories:Programming, python, solver
scoreseq

SCORE-Seq is a command-line program which implements score statistics for detecting disease associations with rare variants in sequencing studies.

Versions:7.1
License:n/a
Categories:Application, Biostatistics
scythe

Scythe is a Bayesian adapter trimmer .

Versions:0.993
License:https://github.com/vsbuffalo/scythe
Categories:Genomics, Sequencing, gene, omics
seqmule

Automated human exome/genome variants detection

Versions:1.2.6
License:GPLv2
Categories:bioinformatics
sicer

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

Versions:1.1
License:GPLv2
Categories:bioinformatics
sickle

A windowed adaptive trimming tool for FASTQ files using quality

Versions:1.33.6
License:MIT software license
Categories:bioinformatics trimming fastq
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Total pages: 10
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