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http://sourceforge.net/projects/b-o-s-s/

Batch primer selection software program designed to select PCR oligos for gap closure for assemblies containing a large number of gaps. It will select oligos for gap closure of both contig and scaffold gaps.

Proper citation: Batch Oligo Selection Script (RRID:SCR_002808) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

Software to access the ArrayExpress Repository at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet

Proper citation: ArrayExpress (R) (RRID:SCR_000120) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dtailor/

A fully extendable software framework, for property-based design of synthetic DNA sequences.

Proper citation: D-Tailor (RRID:SCR_000115) Copy   

•   Source: SciCrunch Registry

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

Software package that helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.

Proper citation: AffyRNADegradation (RRID:SCR_000118) Copy   

•   Source: SciCrunch Registry

http://www.mayo.edu/research/departments-divisions/department-health-sciences-research/division-biomedical-statistics-informatics/software/bioinformatics-software-packages

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. A free bioinformatics software tool to help identify fusion transcripts from paired-end transcriptome sequencing data. The source codes of SnowShoes-FTD are provided in two formats: one configured to run on the Sun Grid Engine for parallelization with shorter run time, and the other formatted to run on a single LINUX node.

Proper citation: SnowsShoes-FTD (RRID:SCR_000076) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/VariantAnnotation.html

Software package to annotate variants, compute amino acid coding changes, and predict coding outcomes.

Proper citation: VariantAnnotation (RRID:SCR_000074) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/SOAPfusion.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 22,2022. An open source software tool for fusion discovery with paired-end RNA-Seq reads. The tool follows a different strategy by finding fusions directly and verifying them, differentiating it from all other existing tools by finding the candidate regions and searching for the fusions afterwards.

Proper citation: SOAPfusion (RRID:SCR_000079) Copy   

•   Source: SciCrunch Registry

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

Software functions for data analysis and graphical displays for developmental microarray time course data.

Proper citation: timecourse (RRID:SCR_000077) Copy   

•   Source: SciCrunch Registry

http://patchwork.r-forge.r-project.org/

Software tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid. Patchwork takes BAM files as input whereas PatchworkCG takes input from CompleteGenomics files. TAPS performs the same analysis as Patchwork but for microarray data.

Proper citation: Patchwork (RRID:SCR_000072) Copy   

•   Source: SciCrunch Registry

http://www.cebitec.uni-bielefeld.de/index.php/2-uncategorised/99-tacoa?highlight=WyJ0YWNvYSJd

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software that can accurately predict the taxonomic origin of genomic fragments from metagenomic data sets by combining the advantages of the k -NN approach with a smoothing kernel function.

Proper citation: TACOA (RRID:SCR_000107) Copy   

•   Source: SciCrunch Registry

http://bioinf.scri.ac.uk/tablet/

A lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments.

Proper citation: Tablet (RRID:SCR_000017) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/sirnarules/

An open-source JAVA program that is surprisingly efficient at predicting active siRNAs.

Proper citation: siRNArules (RRID:SCR_000096) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/abmining/

Python scripts to analyze antibody libraries sequenced by next generation sequencing methods (454, Ion Torrent, MiSeq).

Proper citation: AbMining ToolBox (RRID:SCR_000090) Copy   

•   Source: SciCrunch Registry

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

Desktop application for analysis and visualization of large-scale cell signaling networks.

Proper citation: SNAVI (RRID:SCR_000091) Copy   

•   Source: SciCrunch Registry

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

Software package that provides netCDF storage based methods and functions for manipulation of flow cytometry data.

Proper citation: ncdfFlow (RRID:SCR_000009) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/spdesigner/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An open source software program for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa.

Proper citation: SP-Designer (RRID:SCR_000031) Copy   

•   Source: SciCrunch Registry

https://github.com/brendanofallon/SNPSVM/

A support vector machine for calling variants from next-gen sequencing data. It takes as input a BAM-formatted alignment of sequencing reads, and emits a VCF formatted file describing where all the SNPs (single nucleotide polymorphisms) are.

Proper citation: SNPSVM (RRID:SCR_000028) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mysirna/

Software that integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches.

Proper citation: MysiRNA-designer (RRID:SCR_000102) Copy   

•   Source: SciCrunch Registry

http://microbiology.se/software/megraft/

A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes.

Proper citation: Megraft (RRID:SCR_000240) Copy   

•   Source: SciCrunch Registry