Tools   Select Another Resource Report Type

http://scalpel.sourceforge.net/

A software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina).

Proper citation: Scalpel (RRID:SCR_012107) Copy   

•   Source: SciCrunch Registry

http://xmsanalyzer.sourceforge.net

A software package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. xMSanalyzer comprises of utilities that can be classified into five main modules: 1) merging apLCMS or XCMS sample processing results from multiple sets of parameter settings, 2) evaluation of sample quality, feature consistency, and batch-effect, 3) feature matching, and 4) characterization of m/z using KEGG REST; 5) Batch-effect correction using ComBat.

Proper citation: xMSanalyzer (RRID:SCR_012144) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/freesurf_r/

A software package which contains tools for doing group analysis of FreeSurfer surface data using the general linear model in R (lm). Results can be rendered in FreeSurfer freeview or AFNI SUMA. Plots for selected vertices can be rendered in R with ggplot2.

Proper citation: freesurfR (RRID:SCR_014110) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/minc-toolkit

A set of MINC-based image processing tools packaged together. It includes MINC, N3, BICPL, EBKTS, ANIMAL, INSECT, BEaST, Register, Display, and xdisp.

Proper citation: minc-toolkit (RRID:SCR_014138) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/hammer

A software package which performs high-dimensional warping of brain images. Standard voxel-based analysis can be applied to these tissue density maps, in order to examine regional volumetrics, effects of disease, or correlations with clinical measurements.

Proper citation: HAMMER: Deformable Registration (RRID:SCR_014118) Copy   

•   Source: SciCrunch Registry

http://www.dis-imaging.gr/OLYMPUS/software.html

A collection of 7 individual software packages that all control the Olympus Imaging systems while also providing different individual features including (but not limited to): basic measurement functions, process automation, ratio analysis, and real time image acquisition.

Proper citation: Olympus Cell Software (RRID:SCR_014342) Copy   

•   Source: SciCrunch Registry

http://www.matrixscience.com/server.html

A software package and server used to identify and characterize proteins from primary sequence databases using mass spectrometry data. Mascot integrates peptide mass fingerprinting, sequence querying, and MS/MS ion searching in order to search for proteins in databases like SwissProt, NCBInr, EMBL EST divisions, contaminants, and cRAP. If a license is purchased, users may: search data sets that exceed the 1200 spectrum limit of the free version; set up automated, high throughput work; add and edit proteins and quantification methods; and search a preferred collection of sequence databases. The software package works with instruments from AB Sciex, Agilent, Bruker, Jeol, Shimadzu, Thermo Scientific, and Waters.

Proper citation: Mascot (RRID:SCR_014322) Copy   

•   Source: SciCrunch Registry

https://www.rad.upenn.edu/sbia/software/index.html#hammer

Software package that performs high-dimensional warping of brain images. Standard voxel-based analysis can be applied to these tissue density maps, in order to examine regional volumetrics, effects of disease, or correlations with clinical measurements. In order to make HAMMER as robust as possible to different acquisition protocols and conditions, they provide a distribution that assumes that images have been skull-stripped and segmented into gray matter, white matter, and ventricular CSF. We have other software tools that can perform these steps, including skull stripping, reorientation and reslicing, and segmentation tools. Importantly, they use 250 for WM, 150 for GM, 50 for Ventricles and 10 for CSF in the tissue-segmented brain images. Current modules used for group analysis: Labeling subject brain using a manually-labeled brain Model; Generating RAVENS map for each tissue (WM, GM, VN); Normalizing subject brain images

Proper citation: Hierarchical Attribute Matching Mechanism for Elastic Registration (RRID:SCR_001960) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/brainvox/

An interactive 3D rendering and neuroanatomical analysis package developed for analyzing focal brain lesions and functional brain imaging data (Damasio and Frank, 1991; Frank, Damasio and Grabowski, 1997).

Proper citation: Brainvox (RRID:SCR_009448) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/broccoli/

A software package written in OpenCL (Open Computing Language) that can be used for parallel analysis of fMRI data on a large variety of hardware configurations. If BROCCOLI is running on a GPU, it can perform non-linear spatial normalization to a 1 mm brain template in 4-6 s and run a second level permutation test with 10,000 permutations.

Proper citation: BROCCOLI (RRID:SCR_014093) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/clValid/index.html

An R package which contains functions for validating the results of a clustering analysis.

Proper citation: clValid (RRID:SCR_014626) Copy   

•   Source: SciCrunch Registry

http://www.gromacs.org

Software package created to perform molecular dynamics. Molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. Can also be used for research on non-biological systems, such as polymers.

Proper citation: GROMACS (RRID:SCR_014565) Copy   

•   Source: SciCrunch Registry

http://aatpackage.sourceforge.net/

Genome tool for analyzing and annotating large genomic sequences containing introns. It includes a program for comparing the query sequence with a protein database and another for comparing the query with a cDNA database. The database search program identifies regions of the query sequence that are similar to a database sequence. Then the alignment program constructs an optimal alignment for each region and the database sequence, as well as reports the coordinates of exons in the query sequence. Pairwise alignments of the query sequence with protein and cDNA database sequences are combined into multiple sequence alignments, which provide a view of all protein and cDNA sequences matching a query region.

Proper citation: Analysis and Annotation Tool (AAT) Package (RRID:SCR_014658) Copy   

•   Source: SciCrunch Registry

http://www.biosolveit.de/LeadIT/

Drug discovery platform for medicinal and computational researchers. Users can assess the binding affinity and contributions to binding of a complex, find new scaffolds, grow molecules towards pharmacophore points, link fragments, and investigate possible dock binding conformations.

Proper citation: LeadIT (RRID:SCR_014881) Copy   

•   Source: SciCrunch Registry

http://www.chemcomp.com/MOE-Molecular_Operating_Environment.htm

Drug discovery software package which can be used in structure-based design, fragment-based design, pharmacophore discovery, medicinal chemistry, protein and antibody modelling, and molecular modeling and simulations. Each aspect of the software package has its own unique features: for example, features for structure-based design include active site detection, scaffold replacement, multi fragment search, and solvent analysis.

Proper citation: MOE (RRID:SCR_014882) Copy   

•   Source: SciCrunch Registry

http://hkl-xray.com/

Semi-automatic crystallographic data collection software that integrates data collection, data reduction, phasing and model building in a single software package.

Proper citation: HKL 3000 (RRID:SCR_015023) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/devel/bioc/html/RUVSeq.html

Software package that implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.

Proper citation: RUVSeq (RRID:SCR_006263) Copy   

•   Source: SciCrunch Registry

https://www.schrodinger.com/Prime/

Software package that uses homology modeling and fold recognition to make protein structure predictions.

Proper citation: Prime (RRID:SCR_014887) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/topGO.html

Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.

Proper citation: topGO (RRID:SCR_014798) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/ncdfFlow.html

Software package that provides netCDF storage based methods and functions for manipulation of flow cytometry data.

Proper citation: ncdfFlow (RRID:SCR_000009) Copy   

•   Source: SciCrunch Registry