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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.
https://code.google.com/p/swdmr/
A free software using a sliding-window approach to identify differentially methylated regions (DMR) from whole-genome bisulfite sequencing.
Proper citation: swDMR (RRID:SCR_007316) Copy
http://web.bioinformatics.ic.ac.uk/geb/
A Java application developed to visualise distribution of genomic features in high resolution.
Proper citation: GEB (RRID:SCR_007395) Copy
http://sourceforge.net/projects/taipan/
A fast hybrid short-read assembly tool.
Proper citation: Taipan (RRID:SCR_007330) Copy
http://bmserver.sce.ntu.edu.sg/INVERTER/
Software for a de novo exact match tandem repeat finder which main advantage is without the need to specify either the pattern or a particular pattern size, integrated with a data visualization tool and has a built-in user-friendly Graphical User Interface.
Proper citation: INVERTER (RRID:SCR_007956) Copy
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
Allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser.
Proper citation: BigWig and BigBed (RRID:SCR_007708) Copy
https://code.google.com/p/highssr/
Software that predicts microsatellites with Tandem Repeats Finder (TRF).
Proper citation: HighSSR (RRID:SCR_007949) Copy
http://genotan.sourceforge.net/
A free software tool to identify length variation of microsatellites from short sequence reads.
Proper citation: GenoTan (RRID:SCR_007935) Copy
http://smithlab.usc.edu/histone/rseg/
Software package aimed to analyze ChIP-Seq data, especially for identifying genomic regions and their boundaries marked by diffusive histone modification markers, such as H3K36me3 and H3K27me3.
Proper citation: RSEG (RRID:SCR_007695) Copy
http://www.ebi.ac.uk/huber-srv/hilbert/
Software tool that allows to display very long data vectors in a space-efficient manner, allowing the user to visually judge the large scale structure and distribution of features simultaneously with the rough shape and intensity of individual features.
Proper citation: HilbertVis (RRID:SCR_007862) Copy
A cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.
Proper citation: BRIG (RRID:SCR_007802) Copy
http://web.bioinformatics.cicbiogune.es/AM/AnnotationModules.php
A tool for finding significant combinations of multisource annotations in gene lists.
Proper citation: Annotation-Modules (RRID:SCR_008025) Copy
http://biq-analyzer-ht.bioinf.mpi-inf.mpg.de/
Software that currently allows to process an amount of bisulfite sequencing reads obtained in one or several bisulfite sequencing experiments.
Proper citation: BiQAnalyzer HT (RRID:SCR_008045) Copy
http://erlichlab.wi.mit.edu/lobSTR/
A software tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data.
Proper citation: lobSTR (RRID:SCR_008030) Copy
http://drive5.com/usearch/manual/uchime_algo.html
An algorithm for detecting chimeric sequences.
Proper citation: UCHIME (RRID:SCR_008057) Copy
http://genome-www.stanford.edu/TMA/
Software Tools for High-Throughput Analysis and Archiving of Immunohistochemistry Staining Data Obtained with Tissue Microarrays.
Proper citation: Stanford TMA Software (RRID:SCR_005598) Copy
http://www.compbio.dundee.ac.uk/downloads/oxbench/
A suite of programs aimed at developers of alignment methods rather than end-users to assess the accuracy of multiple sequence alignment methods. It includes a reference database of protein multiple sequence alignments that were generated by consideration of protein three-dimensional structure.
Proper citation: OXBench (RRID:SCR_005591) Copy
http://staden.sourceforge.net/
A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
Proper citation: Staden Package (RRID:SCR_005629) Copy
http://mesquiteproject.org/packages/chromaseq/
A software package in Mesquite that processes chromatograms, makes contigs, base calls, etc., using in part the programs Phred and Phrap.
Proper citation: Chromaseq (RRID:SCR_005587) Copy
https://github.com/phe-bioinformatics/snp-search/tree/master/test_data
A software tool that manages SNP data and outputs useful information which can be used to test important biological hypotheses.
Proper citation: snp-search (RRID:SCR_005618) Copy
http://www.ibridgenetwork.org/wustl/splinter
Software that detects and quantifies short IN/DELs as well as single nucleotide substitutions in pooled-DNA samples.
Proper citation: SPLINTER (RRID:SCR_005826) Copy
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