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http://sourceforge.net/projects/kinannote/
Software that identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine / threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com.
Proper citation: Kinannote (RRID:SCR_000352) Copy
http://sourceforge.net/projects/jnomics/
A collection of cloud-scale DNA sequence analysis tools.
Proper citation: Jnomics (RRID:SCR_000348) Copy
A genome browser framework which gives an open browsing experience, open data access, collaborative work support, and a framework to import annotations. Multiple data access approaches are supported for external platforms to retrieve data from ABrowse. This resource also contains an online user-space in which users can create, store and share comments, annotations and landmarks.
Proper citation: ABrowse (RRID:SCR_000345) Copy
http://icbi.at/software/gpviz/gpviz.shtml
A versatile Java-based software used for dynamic gene-centered visualization of genomic regions and/or variants.
Proper citation: GPViz (RRID:SCR_000346) Copy
http://www.bioconductor.org/packages/release/bioc/html/iASeq.html
Software that uses a Bayesian hierarchical mixture model to learn correlation patterns of allele-specificity among multiple proteins.
Proper citation: iASeq (RRID:SCR_000420) Copy
http://www.bioconductor.org/packages/release/bioc/html/rTANDEM.html
An R/Bioconductor package that interfaces the X!Tandem protein identification algorithm.
Proper citation: rTANDEM (RRID:SCR_000409) Copy
https://sites.google.com/site/beckerjeremie/home/nucleofinder
A software for a statistical approach for the detection of nucleosome positions in a cell population. The software identifies important features of nucleosome organization such as the spacing downstream of active promoters and the enrichment and depletion of GC/AT dinucleotides of in vitro nucleosomes.
Proper citation: NucleoFinder (RRID:SCR_000368) Copy
https://github.com/yongchao/flowPeaks
Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.
Proper citation: flowPeaks (RRID:SCR_000407) Copy
http://proteinprophet.sourceforge.net/
Software that automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST.
Proper citation: ProteinProphet (RRID:SCR_000286) Copy
https://github.com/mickaelleclercq/mirdup
A software used for the validation of pre-miRNAs predictions as well as predict the final structure of mature miRNA.
Proper citation: MiRdup (RRID:SCR_000316) Copy
http://www.bioconductor.org/packages/release/bioc/html/QUALIFIER.html
Software that provides quality control and quality assessment tools for gated flow cytometry data.
Proper citation: QUALIFIER (RRID:SCR_000389) Copy
http://sourceforge.net/projects/fqzcomp/
A basic fastq compressor, designed primarily for high performance.
Proper citation: fqzcomp (RRID:SCR_000299) Copy
http://sourceforge.net/projects/mirprimer/
Software tool for automatic design of primers for PCR amplification of microRNAs using the method miR-specific RT-qPCR (Balcells, I., Cirera, S., and Busk, P.K. (2011). Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers. BMC Biotechnol. 11, 70).
Proper citation: miRprimer (RRID:SCR_000480) Copy
http://sourceforge.net/projects/pyqpcr/
A GUI application written in python that deals with quantitative PCR (QPCR) raw data. Using quantification cycle values extracted from QPCR instruments, it uses a proven and universally applicable model to give finalized quantification resu
Proper citation: pyQPCR (RRID:SCR_000471) Copy
Software tool for association study of high-dimensional microRNA expression data with repeated measures. The penalized regression model incorporates a grid search method for analyzing associations of high-dimensional microRNA expression data with repeated measures.
Proper citation: PGS (RRID:SCR_000475) Copy
https://github.com/cc2qe/speedseq
Software for a lightweight, flexible, and open source pipeline that identifies genomic variation (single nucleotide variants (SNVs), indels, and structural variants (SVs)).
Proper citation: SpeedSeq (RRID:SCR_000469) Copy
https://github.com/yhwu/matchclips/
Software program that detects the precise break points of Copy number variations (CNVs) through a fuzzy string matching algorithm using both CIGAR and POS information. In case the two break points of a CNV are in repeated regions and the break points are not unique, it reports the range where the break points can slide.
Proper citation: MATCHCLIP (RRID:SCR_000541) Copy
http://www.bioconductor.org/packages/release/bioc/html/TDARACNE.html
Software package to infer gene regulatory networks from time-series measurements. The algorithm is expected to be useful in reconstruction of small biological directed networks from time course data.
Proper citation: TDARACNE (RRID:SCR_000498) Copy
Software package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Mfuzz (RRID:SCR_000523) Copy
http://gmt.genome.wustl.edu/pindel/0.2.4/
Software to detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Pindel (RRID:SCR_000560) Copy
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