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https://CRAN.R-project.org/package=mitml
Software R package for multiple imputation of missing data in multilevel modeling.
Proper citation: mitml (RRID:SCR_024516) Copy
http://www.drive5.com/muscle/prefab.htm
Downloadable data designed for testing multiple sequence alignment methods.
Proper citation: PREFAB (RRID:SCR_001009) Copy
http://www.definiens.com/research/tissue-studio/developer-xd
A development environment designed to create automated image analysis solutions for segmentation and classification tasks. It delivers quantitative and consistent data for any type of image (e.g., IHC, ISH, IF images in different formats). Developer XD also contains a large library of image analysis algorithms, which users can add to, for whole slide images and tissue microarrays (TMAs). It can be integrated with an existing Tissue Studio installation.
Proper citation: Definiens Developer XD (RRID:SCR_014283) Copy
https://cab.spbu.ru/software/spades/
Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: SPAdes (RRID:SCR_000131) Copy
Software suite of automated docking tools. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure. AutoDock consist of AutoDock 4 and AutoDock Vina. AutoDock 4 consists of autodock to perform docking of ligand to set of grids describing target protein, and autogrid to pre calculate these grids.
Proper citation: AutoDock (RRID:SCR_012746) Copy
http://www.bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html
Software package that includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements.
Proper citation: ChIPpeakAnno (RRID:SCR_012828) Copy
Software tool 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). Currently over 56% of human genomic sequence is identified and masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including nhmmer, cross_match, ABBlast/WUBlast, RMBlast and Decypher. RepeatMasker makes use of curated libraries of repeats and currently supports Dfam ( profile HMM library ) and RepBase ( consensus sequence library ).
Proper citation: RepeatMasker (RRID:SCR_012954) Copy
http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss
A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.
Proper citation: Trans-ABySS (RRID:SCR_013322) Copy
http://www.eisenlab.org/eisen/?page_id=42
Software to graphically browse results of clustering and other analyses from Cluster.
Proper citation: TreeView (RRID:SCR_013503) Copy
http://www.broadinstitute.org/igv/
A high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
Proper citation: Integrative Genomics Viewer (RRID:SCR_011793) Copy
https://CRAN.R-project.org/package=cluster
Software R package. Methods for Cluster analysis. Performs variety of types of cluster analysis and other types of processing on large microarray datasets.
Proper citation: Cluster (RRID:SCR_013505) Copy
https://CRAN.R-project.org/package=survival
Software R package contains core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.
Proper citation: survival (RRID:SCR_021137) Copy
https://CRAN.R-project.org/package=caret
Software R package provides misc functions for training and plotting classification and regression models.Contains tools for data splitting, pre-processing, feature selection, model tuning using resampling, and variable importance estimation, as well as other functionality.
Proper citation: caret (RRID:SCR_021138) Copy
Issue
https://reich.hms.harvard.edu/software
EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker''s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. Source code, documentation and executables for using EIGENSOFT 3.0 on a Linux platform can be downloaded. New features of EIGENSOFT 3.0 include supporting either 32-bit or 64-bit Linux machines, a utility to merge different data sets, a utility to identify related samples (accounting for population structure), and supporting multiple file formats for EIGENSTRAT stratification correction.
Proper citation: Eigensoft (RRID:SCR_004965) Copy
https://github.com/Illumina/strelka/
Software for somatic single nucleotide variant (SNV) and small indel detection from sequencing data of matched tumor-normal samples. Strelka2 germline and somatic small variant caller.
Proper citation: Strelka2 (RRID:SCR_005109) Copy
http://bioinf.cs.ucl.ac.uk/downloads/MetaPSICOV/
Software tool for accurate prediction of contacts and long range hydrogen bonding in proteins.
Proper citation: MetaPSICOV (RRID:SCR_024517) Copy
https://mathgen.stats.ox.ac.uk/impute/impute.html
Software application for estimating (imputing) unobserved genotypes in SNP association studies. The program is designed to work seamlessly with the output of the genotype calling program CHIAMO and the population genetic simulator HAPGEN, and it produces output that can be analyzed using the program SNPTEST. (entry from Genetic Analysis Software)
Proper citation: IMPUTE (RRID:SCR_009245) Copy
Software application that provides researchers with the tools necessary for various types of statistical genetic analysis of human family data. (entry from Genetic Analysis Software)
Proper citation: SAGE (RRID:SCR_009302) Copy
http://www.pstnet.com/eprime.cfm
A suite of applications to fulfill all of your computerized experiment needs. Used by more than 15,000 professionals in the research community, E-Prime provides a truly easy-to-use environment for computerized experiment design, data collection, and analysis. E-Prime provides millisecond precision timing to ensure the accuracy of your data. E-Prime's flexibility to create simple to complex experiments is ideal for both novice and advanced users. The E-Prime suite of applications includes: * E-Studio ? Drag and drop graphical interface for experiment design * E-Basic ? Underlying scripting language of E-Prime * E-Run ? Once the experiment is generated with a single click, E-Run affords you the millisecond precision of stimulus presentation, synchronizations, and data collection. * E-Merge ? Merges your single session data files for group analysis * E-DataAid ? Data management utility * E-Recovery ? Recovers data files
Proper citation: E-Prime (RRID:SCR_009567) Copy
http://archive.broadinstitute.org/mpg/tagger/
Software application (entry from Genetic Analysis Software)
Proper citation: TAGGER (RRID:SCR_009419) Copy
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