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http://chiulab.ucsf.edu/surpi/

Software providing a computational pipeline for pathogen identification from complex metagenomic next-generation sequencing (NGS) data generated from clinical samples.

Proper citation: SURPI (RRID:SCR_003071) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/fas-dpd/

Software program to design degenerate primers for PCR.

Proper citation: FAS-DPD (RRID:SCR_003068) Copy   

•   Source: SciCrunch Registry

http://pfind.ict.ac.cn/software/pFind/index.html

A search engine system for automated peptide and protein identification from tandem mass spectra.

Proper citation: pFind (RRID:SCR_003011) Copy   

•   Source: SciCrunch Registry

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

Software for differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions.

Proper citation: tweeDEseq (RRID:SCR_003038) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/isopat/

Software function that calculates the isotopic pattern (fine structures) for a given chemical formula.

Proper citation: Isopat (RRID:SCR_003025) Copy   

•   Source: SciCrunch Registry

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

Software package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S).

Proper citation: BRAIN (RRID:SCR_003018) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/sasqpcr/

All-in-one computer program for robust and rapid analysis of quantitative reverse transcription real-time polymerase chain reaction (RT-qPCR) data in SAS. It incorporates all functions important for RT-qPCR data analysis including assessment of PCR efficiencies, validation of internal reference genes and normalizers, normalization of confounding variations across samples and statistical comparisons of target gene expression in parallel samples. The program is highly automatic in data analyses and result output. The input data have no limitations for the number of genes or cDNA samples. Users can simply change the macro variables to test various analytical strategies, optimize results and customize the analytical processes. The program is also extendable allowing advanced SAS users to develop particular statistical tests appropriate for their experimental designs. Thus users are the actual decision-makers controlling RT-qPCR data analyses. The program has to be used in SAS software; however, extensive SAS programming knowledge is not required.

Proper citation: SASqPCR (RRID:SCR_003056) Copy   

•   Source: SciCrunch Registry

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

R package providing functions to assess and to compare the performance of risk prediction (survival) models.

Proper citation: SurvComp (RRID:SCR_003054) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/ptw/

Software that aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS (Root Mean Square error) and WCC (Weighted Cross Correlation).

Proper citation: Parametric Time Warping (RRID:SCR_003053) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/gutentag/

An interactive, user-editable genetic sequence database tool, targeted at molecular biology research groups that can be browsed using tags. The tool is Web 2.0-flavoured, allowing users to do more than just retrieve information. Its focus on user-editability is supported by the use of tags (metadata) associated with genetic sequences. Several methods of retrieving stored data are available including tag-clouds, BLAST and keyword searches. Also, sequence tags related to HGNC gene names, conserved domains (CDD) and GO terms can be automatically generated given sequence data. The tool is constructed using the high-level Python web framework, Django, with a SQLite3 backend.

Proper citation: Gutentag (RRID:SCR_003051) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/pacBioToCA

A module in the Celera Assembler software package that performs error correction on PacBio long reads by mapping shorter, high accuracy reads onto the long reads.

Proper citation: PacBioToCA (RRID:SCR_003044) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/R-pbutils

An R software package providing plotting and convenience functions.

Proper citation: R-pbutils (RRID:SCR_002995) Copy   

•   Source: SciCrunch Registry

http://wiki.solariseclipse.net/PrimerDesigner

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Software program to aid in designing of primers and creation of primer sheets. The program allows users to select a background and enter mutaions. An initial primer is then suggested. User can manipulate the selected primer to add or remove nucleotides from either 5? or 3? ends. A set of parameters reflecting the goodness of the primer is updated on the fly, as the user makes changes. Once happy with the primer, the information is saved in a primer sheet, which can then be uploaded to the BGME lab primer database on the Wiki.

Proper citation: Primer Designer (RRID:SCR_003189) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/salt1/

Software that can accurately and sensitivity classify short reads of next-generation sequencing (NGS) into protein domain families. It is based on profile HMM and a supervised graph contribution algorithm. Compared to existing tools, it has high sensitivity and specificity in classifying short reads into their native domain families.

Proper citation: SALT (RRID:SCR_003187) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/xorro-overlap/

Efficient paired-read overlap software program for use with Illumina sequencing.

Proper citation: XORRO (RRID:SCR_003181) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.sfu.ca/software-novelseq

Software pipeline to detect novel sequence insertions using high throughput paired-end whole genome sequencing data.

Proper citation: NovelSeq (RRID:SCR_003136) Copy   

•   Source: SciCrunch Registry

http://mrcanavar.sourceforge.net/

Copy number caller that analyzes the whole-genome next-generation sequence mapping read depth to discover large segmental duplications and deletions. It also has the capability of predicting absolute copy numbers of genomic intervals.

Proper citation: mrCaNaVaR (RRID:SCR_003135) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/saskprimerfs/

Software pipeline for designing gene family specific PCR primers. It infers intronic regions of a target species and design for them by utilizing DNA sequence information from a reference organism.

Proper citation: SaskPrimerFS (RRID:SCR_003159) Copy   

•   Source: SciCrunch Registry

https://github.com/brunonevado/Pipeliner

Software for evaluating the performance of bioinformatics pipelines for Next Generation re-Sequencing.

Proper citation: Pipeliner (RRID:SCR_003171) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.rutgers.edu/Software/SLiQ/

Software for simple linear inequalities based Mate-Pair reads filtering and scaffolding. A set of simple linear inequalities (SLIQ) derived from the geometry of contigs on the line that can be used to predict the relative positions and orientations of contigs from individual mate pair reads and thus produce a contig digraph. The SLIQ inequalities can also filter out unreliable mate pairs and can be used as a pre-processing step for any scaffolding algorithm. This tool filters mate pairs and then produces a Directed Contig Graph (contig diGraph). Also provided is a Naive scaffolder that can then produce scaffolds out of the contig diGraph.

Proper citation: SLIQ (RRID:SCR_005003) Copy   

•   Source: SciCrunch Registry