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Rgeospatial-h4

R environment for geospatial statistics

Versions:3.5.0
License:GPL, https://www.r-project.org/Licenses/
Categories:Geospatial, data science, graphics, statistics
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:3.5.1; 3.3.0; 3.4.2; 3.3.3
License:GPL, https://www.r-project.org/Licenses/
Categories:big data, data science, graphics, statistics
RNAhybrid

RNAhybrid is a tool for finding minimum free energy hybridization of a long (target) and a short (query) RNA. The hybridization is performed in a kind of domain mode, ie. the short sequence is hybridized to the best fitting parts of the long one. The tool is primarily meant as a means for microRNA target prediction.

Versions:2.1.2
License:GPLv2
Categories:bioinformatics
Rneuropointillist

Flexible modeling of neuroimaging data in R

Versions:3.5.0
License:MIT, https://github.com/IBIC/neuropointillist/blob/master/LICENSE
Categories:MRI, R, fMRI, longitudinal, neuroimaging, structural equation model
roary

Roary is a high speed stand alone pan genome pipeline

Versions:3.7.0; 3.12.0
License:GPLv3
Categories:bioinformatics
rosetta

Rosetta is a very large software suite for macromolecular modeling.

Versions:3.9; 3.7
License:GPLv2
Categories:bioinformatics
rsem

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

Versions:1.3.1; 1.2.31
License:GPLv3
Categories:bioinformatics
rseqc

RSeQC: An RNA-seq Quality Control Package

Versions:2.3.7
License:GPLv2
Categories:bioinformatics
RStudio-desktop

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

Versions:1.1.201; 1.1.419
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; 1.1.456; 1.1.201; 1.1.419; 1.0.44
License:AGPL
Categories:ARC Connect, IDE, big data, data science, graphics, statistics, web
Rtidyverse

R environment for statistical computing and graphics

Versions:3.5.0; 3.5.1
License:GPL, https://www.r-project.org/Licenses/
Categories:big data, data science, graphics, statistics
rvtests

a flexible software package for genetic association analysis for sequence datasets

Versions:2017.1009
License:GPLv2
Categories:bioinformatics
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; 0.9.1; 0.11.3
License:GPLv3
Categories:bioinformatics
samtools

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

Versions:1.9; 0.1.18; 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
Seissol

SETSM: fully automatic algorithm for deriving Digital Terrain Models (DTM) from pairs of satellite imagery

Versions:2018.11 with intel/17.0.1
License:Apache 2.0
Categories:Mapping
selectionStats

This script calculates diversity and selection statistics for fasta alignments.

Versions:1.0
License:MIT
Categories:bioinformatics
seqkit

SeqKit is a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

Versions:0.10.2
License:MIT
Categories:bioinformatics
seqmule

Automated human exome/genome variants detection

Versions:1.2.6
License:GPLv2
Categories:bioinformatics
SETSM

SETSM: fully automatic algorithm for deriving Digital Terrain Models (DTM) from pairs of satellite imagery

Versions:3.3.1 with intel/3.3.1
License:Apache 2.0
Categories:Mapping
seurat

R library Seurat

Versions:3.0
License:GPLv2
Categories:bioinformatics
sga

SGA – String Graph Assembler

Versions:0.10.15
License:GPL
Categories:Genomics
shapeit2

a fast and accurate method for estimation of haplotypes

Versions:2.17
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
siesta

SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

Versions:4.1-b3
License:Electronic Structure, ab initio, quantum, dft
Categories:
sift4g

SIFT 4G takes a query sequence and uses multiple alignment information to predict tolerated and deleterious substitutions for every position of the query sequence.

Versions:2.0.0
License:GPLv2
Categories:bioinformatics
slepc

SLEPc, the Scalable Library for Eigenvalue Problem Computations. The library is used to compute eigenvalues and eigenvectors of large, sparse matrices with iterative methods.

Versions:3.8.3; 3.7.4
License:GNU LGPL license
Categories:eigenvalues, eigenvectors
smrtanalysis

A software suite designed for use with Single Molecule, Real-Time (SMRT) Sequencing data.

Versions:2.3.0
License:GPLv2
Categories:bioinformatics
SNAP

SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.

Versions:2013-11-29
License:MIT (https://opensource.org/licenses/MIT)
Categories:Gene finding, HMM, eukaryotic genome, prokaryotic genome
soapdenovo2

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler.

Versions:2.04-r241
License:GPL
Categories:Genomics
somaticsniper

The purpose of this program is to identify single nucleotide positions that are different between tumor and normal

Versions:1.0.5.0
License:GPLv2
Categories:bioinformatics
sonnet

[SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] EnSight is a post processing and visualization tool.

Versions:16.0
License:https://www.sonnetsoftware.com/products/lite/license.html
Categories:design, simulation
Current page: 11
Total pages: 13
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