Tools   Select Another Resource Report Type

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/brantp/rtd

Reference-free ddRADseq analysis software tools. The pipeline script generates reference-sorted, indexed BAM from uniqued reads from radtag sequencing lanes.

Proper citation: rtd (RRID:SCR_000337) Copy   

•   Source: SciCrunch Registry

https://www.infoquant.com/oneclickcgh

Platform-independent array copy number analysis software that provides straightforward yet comprehensive detection and reporting of copy number changes.

Proper citation: oneClickCGH (RRID:SCR_000294) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/fqzcomp/

A basic fastq compressor, designed primarily for high performance.

Proper citation: fqzcomp (RRID:SCR_000299) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bait/

Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data.

Proper citation: BAIT (RRID:SCR_000511) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://fulxie.0fees.us/?type=reference&ckattempt=1

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Web-based tool for evaluating and screening reference genes from extensive experimental datasets. It integrates major computational programs (geNorm, Normfinder, BestKeeper, and the comparative delta-Ct method) to compare and rank the tested candidate reference genes. Based on the rankings from each program, it assigns an appropriate weight to an individual gene and calculated the geometric mean of their weights for the overall final ranking., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RefFinder (RRID:SCR_000472) Copy   

•   Source: SciCrunch Registry

https://github.com/feizhe/PGS

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.atgc-montpellier.fr/mpscan/

Web tool for index free mapping of multiple short reads on a genome.

Proper citation: MPscan (RRID:SCR_000587) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://mfuzz.sysbiolab.eu/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/genome_bio/siphy/

Software that implements rigorous statistical tests to detect bases under selection from a multiple alignment data. It takes full advantage of deeply sequenced phylogenies to estimate both unlikely substitution patterns as well as slowdowns or accelerations in mutation rates. It can be applied as an Hidden Markov Model (HMM), in sliding windows, or to specific regions.

Proper citation: SiPhy (RRID:SCR_000564) Copy   

•   Source: SciCrunch Registry

https://github.com/NetherlandsMetabolomicsCentre/TNO-DECO

Matlab code for preprocessing gas chromatography mass spectrometry data.

Proper citation: TNO-DECO (RRID:SCR_000440) Copy   

•   Source: SciCrunch Registry

http://edwards.sdsu.edu/scaffold_builder/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Tool designed to generate scaffolds (super contigs of sequences joined by N-bases) using the homology provided by a closely related reference sequence. Scaffold_builder is an advanced wrapper for Nucmer, written in Python that resolves several situations that may arise when mapping contigs to the reference genome.

Proper citation: Scaffold builder (RRID:SCR_000556) Copy   

•   Source: SciCrunch Registry