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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
An R package for analyzing large Affymetrix data sets.
Proper citation: Aroma.affymetrix (RRID:SCR_010919) Copy
https://github.com/mpyatkov/sbars
Bioinformatics tool for searching different types of long repeats in sequences comparable by size with chromosomes.
Proper citation: SBARS (RRID:SCR_002371) Copy
http://www.bioconductor.org/packages/release/bioc/html/CAMERA.html
A Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data.
Proper citation: CAMERA - Collection of annotation related methods for mass spectrometry data (RRID:SCR_002466) Copy
http://droog.gs.washington.edu/polyphred/
Software program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions. Its functions are integrated with the use of three other programs: Phred (Brent Ewing and Phil Green), Phrap (Phil Green), and Consed (David Gordon and Phil Green). PolyPhred identifies potential heterozygotes using the base calls and peak information provided by Phred and the sequence alignments provided by Phrap. Potential heterozygotes identified by PolyPhred are marked for rapid inspection using the Consed tool.
Proper citation: PolyPhred (RRID:SCR_002337) Copy
http://cran.r-project.org/web/packages/isa2/
A biclustering algorithm that finds modules in an input matrix. A module or bicluster is a block of the reordered input matrix.
Proper citation: Iterative Signature Algorithm (RRID:SCR_002327) Copy
http://kirchnerlab.github.io/libmgf/
A flex/bison-based C++ Mascot Generic Format (MGF) parser library.
Proper citation: libmgf (RRID:SCR_002664) Copy
http://cran.r-project.org/web/packages/ExomeDepth/
Software that calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.
Proper citation: ExomeDepth (RRID:SCR_002663) Copy
http://www.bioconductor.org/packages/devel/bioc/html/MethylAid.html
Software for visual and interactive quality control of large Illumina 450k data sets. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.
Proper citation: MethylAid (RRID:SCR_002659) Copy
https://github.com/rcanovas/libCSAM
Contains several C++ codes for compress, decompress, and access each of the fields of any SAM format file.
Proper citation: libCSAM (RRID:SCR_002766) Copy
https://github.com/lh3/ropebwt2
A software tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo-BWT position by position, starting from the end of the sequences. This algorithm can be largely considered a mixture of BCR and dynamic FM-index. Nonetheless, ropeBWT2 is unique in that it may implicitly sort the input into reverse lexicographical order (RLO) or reverse-complement lexicographical order (RCLO) while building the index.
Proper citation: RopeBWT2 (RRID:SCR_002673) Copy
https://github.com/ahmohamed/NetPathMiner
Software that implements a flexible module-based process flow for network path mining and visualization, which can be fully inte-grated with user-customized functions. It supports construction of various types of genome scale networks from three different pathway file formats (KGML, SBML and BioPAX), enabling its utility to most common pathway databases. In addition, it provides different visualization techniques to facilitate the analysis of even thousands of output paths.
Proper citation: NetPathMiner (RRID:SCR_002757) Copy
Model-based, open source software analysis tool for chromatin states prediction based on time-course epigenetic marks data. It uses a combinatory Finite Mixture model nested with HMM to model the time course marks data in which each single hidden markov model describes the hidden states for a region set across different time points.
Proper citation: GATE (RRID:SCR_002756) Copy
http://pfind.ict.ac.cn/software/pNovo/index.html
A de novo peptide sequencing algorithm using complementary higher-energy collisional dissociation (HCD) and electron transfer dissociation (ETD) tandem mass spectra.
Proper citation: pNovo+ (RRID:SCR_002860) Copy
https://github.com/telatin/covtobed
Software tool to generate BED coverage tracks from BAM files.
Proper citation: covtobed (RRID:SCR_023998) Copy
https://www.gnumed.de/documentation/
Software to build Electronic Medical Record in multiple languages to assist and improve longitudinal care specifically in ambulatory settings.Useful to anyone documenting the health of patients including,doctors, physical therapists, occupational therapists,acupuncturists, nurses, psychologists.
Proper citation: GNUmed (RRID:SCR_024029) Copy
http://ruby.chemie.uni-freiburg.de/~martin/chemtool/
Software tool for drawing organic molecules. Runs under the X Window System using the GTK widget set. Used for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11.
Proper citation: Chemtool (RRID:SCR_023992) Copy
Software tool provides graphical interface for tethered shooting, aka taking photographs with digital camera completely controlled from the computer.
Proper citation: Entangle (RRID:SCR_024015) Copy
https://sourceforge.net/projects/ffp-phylogeny/
Softwaare alignment free comparison tool for phylogenetic analysis and text comparison. Can be applied to nucleotide sequences, complete genomes, proteomes and for text comparison.
Proper citation: FFP (RRID:SCR_024018) Copy
https://github.com/danielhuson/dendroscope3
Software Java program for analyzing and visualizing rooted phylogenetic trees and networks.
Proper citation: Dendroscope3 (RRID:SCR_024003) Copy
https://github.com/GregoryFaust/yaha
Software tool as fast and flexible long read alignment with optimal breakpoint detection.
Proper citation: yaha (RRID:SCR_024365) Copy
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