Software Item | Details | ||||||
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Rgeospatial-h4 | R environment for geospatial statistics
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Rgputools | R gputools library
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rmblast | RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite.
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Rmkl | R environment for statistical computing and graphics
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Rmpi | R environment for statistical computing and graphics
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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.
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Rneuropointillist | Flexible modeling of neuroimaging data in R
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roary | Roary is a high speed stand alone pan genome pipeline
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rosetta | Rosetta is a very large software suite for macromolecular modeling.
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rsem | RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.
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rseqc | RSeQC: An RNA-seq Quality Control Package
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RStudio-desktop | RStudio Server IDE is a powerful and productive user interface for R.
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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/ )
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Rtidyverse | R environment for statistical computing and graphics
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rvtests | a flexible software package for genetic association analysis for sequence datasets
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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.
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salmon | Salmon is a tool for wicked-fast transcript quantification from RNA-seq data.
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samtools | SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.
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sas | SAS statistical system software.
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scipy-dev | Scientific libraries for use within Python.
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scoreseq | SCORE-Seq is a command-line program which implements score statistics for detecting disease associations with rare variants in sequencing studies.
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scythe | Scythe is a Bayesian adapter trimmer .
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Seissol | SETSM: fully automatic algorithm for deriving Digital Terrain Models (DTM) from pairs of satellite imagery
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selectionStats | This script calculates diversity and selection statistics for fasta alignments.
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seqkit | SeqKit is a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
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seqmule | Automated human exome/genome variants detection
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SETSM | SETSM: fully automatic algorithm for deriving Digital Terrain Models (DTM) from pairs of satellite imagery
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seurat | R library Seurat
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sga | SGA – String Graph Assembler
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shapeit2 | a fast and accurate method for estimation of haplotypes
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sicer | A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
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sickle | A windowed adaptive trimming tool for FASTQ files using quality
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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.
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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.
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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.
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smrtanalysis | A software suite designed for use with Single Molecule, Real-Time (SMRT) Sequencing data.
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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.
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soapdenovo2 | SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler.
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somaticsniper | The purpose of this program is to identify single nucleotide positions that are different between tumor and normal
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sonnet | [SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] EnSight is a post processing and visualization tool.
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Total pages: 13
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