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https://code.google.com/p/gel2de/

Software application for performing pixel-by-pixel correlation analysis on a set of gel images from two-dimensional gel electrophoresis and a set of clinical parameters for a population. The application is written in C++, and has been tested on Windows, although it in principle should compile cross platform using CMake.

Proper citation: Gel2DE (RRID:SCR_002977) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.babraham.ac.uk/projects/chipmonk/

Software tool to visualize and analyse ChIP-on-chip array data. Main features: * Import of data from Nimblegen arrays (other formats can be added if people send us examples) * Normalization of data (both per array and per probe) * Various data plotting options to assess data quality and the effectiveness of normalization * Creation of data groups for visualization and analysis * Visualization of data against an annotated genome. * Statistical analysis of data to find probes of interest * Creation of reports containing probes, data and genome annotation Note: This project is no longer being developed, but critical bug fixes will still be provided

Proper citation: ChIPMonk (RRID:SCR_002975) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/DevNet/wiki/SMRT-View

An open source Genome Browser that visualizes data generated by PacBio Sequencing Systems. * Users can explore and interact with all types of analysis results, including resequencing, De novo, cDNA, and barcoding. * Users can also visualize base modifications, base identification and motifs analysis results.

Proper citation: SMRT View (RRID:SCR_003029) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/pbh5tools

Software tools for manipulating HDF5 files produced by Pacific Biosciences. Specifically, this package provides functionality for manipulating and extracting data from cmp.h5 and bas.h5 files.

Proper citation: pbh5tools (RRID:SCR_003027) Copy   

•   Source: SciCrunch Registry

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

A quantitative proteomics software program for accurate protein abundance ratio estimation with confidence interval evaluation.

Proper citation: ProRata (RRID:SCR_002988) Copy   

•   Source: SciCrunch Registry

http://mrsfast.sourceforge.net/

A cache-oblivious algorithm designed to map short reads to reference genome assemblies in a fast and memory-efficient manner. It optimizes cache usage to get higher performance. Currently Supported Features: * Mistmatches, No indels * Paired-end Mapping Mode * Discordant Paired-end Mapping Mode (to be used in conjuction with Variation Hunter)

Proper citation: mrsFAST (RRID:SCR_003128) Copy   

•   Source: SciCrunch Registry

http://splicq.sourceforge.net/

A Java software package which allows for the identification of splicing events and differentially expressed isoforms in next generation sequencing data.

Proper citation: SpliCQ (RRID:SCR_003266) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/orfer/

An extended software package for high throughput PCR primer design for biological sequences. It reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number.

Proper citation: ORFprimer (RRID:SCR_003269) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/gemi/

Automated software tool to design polymerase chain reaction (PCR) primers. It accepts multiple aligned and long sequences with degenerated nucleotides. It can be used for quantitative/real-time PCR, conventional and Sanger sequencing. Gemi accepts DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). The programs are as the following: # The first program is to design PCR primers from multiple sequence alignment. # Program to convert ClustalW format (.aln), Phylip (.phy) and (.gde) formats to Fasta format. # Reverse and/or complement program is to find the reverse and complement counterpart of single or multiple sequences.

Proper citation: Gemi (RRID:SCR_003211) Copy   

•   Source: SciCrunch Registry

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

Software package for quantitative DNA sequencing for chromosomal aberrations providing a robust, cost-effective WGS method for DNA copy number analysis. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.

Proper citation: QDNAseq (RRID:SCR_003174) Copy   

•   Source: SciCrunch Registry

http://www.popgen.dk/software/index.php/NgsAdmix

A tool for finding admixture proportions from next generation sequencing (NGS) data that is based on genotype likelihoods. It is a multithreaded c/c++ program.

Proper citation: NGSadmix (RRID:SCR_003208) Copy   

•   Source: SciCrunch Registry

http://compgen.bscb.cornell.edu/phast/

A freely available software package for comparative and evolutionary genomics that consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations. For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. It consists of over 60,000 lines of C code.

Proper citation: PHAST (RRID:SCR_003204) Copy   

•   Source: SciCrunch Registry

https://github.com/hangelwen/miR-PREFeR

An accurate, fast, and easy-to-use plant miRNA prediction software tool using small RNA-Seq data. It utilizes expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species.

Proper citation: miR-PREFeR (RRID:SCR_003353) Copy   

•   Source: SciCrunch Registry

http://www.pictar.org

An algorithm for the identification of microRNA targets. Details are provided (3' UTR alignments with predicted sites, links to various public databases etc) regarding: # microRNA target predictions in vertebrates (Krek et al, Nature Genetics 37:495-500 (2005)) # microRNA target predictions in seven Drosophila species (Grn et al, PLoS Comp. Biol. 1:e13 (2005)) # microRNA targets in three nematode species (Lall et al, Current Biology 16, 1-12 (2006)) # human microRNA targets that are not conserved but co-expressed (i.e. the microRNA and mRNA are expressed in the same tissue) (Chen and Rajewsky, Nat Genet 38, 1452-1456 (2006)) co-expressed targets

Proper citation: PicTar (RRID:SCR_003343) Copy   

•   Source: SciCrunch Registry

https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust

Software for efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles.

Proper citation: BlockClust (RRID:SCR_003347) Copy   

•   Source: SciCrunch Registry

http://geoss.sourceforge.net/

A complete software system used to store and analyze gene expression data.

Proper citation: GEOSS (RRID:SCR_003401) Copy   

•   Source: SciCrunch Registry

https://github.com/mozack/abra

Software that is a realigner for next generation sequencing data. It uses localized assembly and global realignment to align reads more accurately, thus improving downstream analysis (detection of indels and complex variants in particular).

Proper citation: Assembly Based ReAligner (RRID:SCR_003277) Copy   

•   Source: SciCrunch Registry

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

Software package providing functions for the selection of optimal reference genes and the normalization of real-time quantitative PCR data.

Proper citation: NormqPCR (RRID:SCR_003388) Copy   

•   Source: SciCrunch Registry

http://www.gene-quantification.de/bestkeeper.html

Excel-based tool using pair-wise correlations for determination of stable housekeeping genes, differentially regulated target genes and sample integrity. It determines the best suited standards, out of ten candidates, and combines them into an index. The index can be compared with further ten target genes to decide, whether they are differentially expressed under an applied treatment. All data processing is based on crossing points.

Proper citation: BestKeeper (RRID:SCR_003380) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/amplicon/

Software tool for designing PCR primers on aligned groups of DNA sequences. The most important application is the design of "group-specific" PCR primer sets that amplify a DNA region from a given taxonomic group but do not amplify orthologous regions from other taxonomic groups. It is written in Python 2.3 and Tkinter 8.4. The current script was created for Windows and an executable is available. Future versions of the script should be able to run on Linux and Mac

Proper citation: Amplicon (RRID:SCR_003294) Copy   

•   Source: SciCrunch Registry