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http://broadinstitute.github.io/picard/

Java toolset for working with next generation sequencing data in the BAM format.

Proper citation: Picard (RRID:SCR_006525) Copy   

•   Source: SciCrunch Registry

http://www.biopieces.org

A collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in such a way that the data stream can be passed through several different Biopieces, each performing one specific task: modifying or adding records to the data stream, creating plots, or uploading data to databases and web services. The Biopieces are executed in a command line environment where the data stream is initialized by specific Biopieces which read data from files, databases, or web services, and output records to the data stream that is passed to downstream Biopieces until the data stream is terminated at the end of the analysis. The advantage of the Biopieces is that a user can easily solve simple and complex tasks without having any programming experience. Moreover, since the data format used to pass data between Biopieces is text based, different developers can quickly create new Biopieces in their favorite programming language - and all the Biopieces will maintain compatibility. Finally, templates exist for creating new Biopieces in Perl and Ruby. There are currently ~190 Biopieces (March 2014).

Proper citation: Biopieces (RRID:SCR_005783) Copy   

•   Source: SciCrunch Registry

http://www.leicabiosystems.com/index.php?id=9161

A high performance, intuitive client viewer with integrated reporting functionality that can be used as a standalone viewer for accessing slides locally, or connected to Digital Image Hub for remote review.

Proper citation: Slidepath (RRID:SCR_005597) Copy   

•   Source: SciCrunch Registry

http://www.geospiza.com/Products/finchtv.shtml

Chromatogram viewer that can display an entire trace in a scalable multi-pane view, allows raw data views, BLAST searching and the ability to reverse complement sequences and traces., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: FinchTV (RRID:SCR_005584) Copy   

•   Source: SciCrunch Registry

http://www.geneious.com/features/microsatellite-analysis

Free plugin that imports ABI fragment analysis ?les and allows you to visualize traces, ?t ladders, call peaks, predict bins, display alleles in a tabular format and export your data.

Proper citation: Geneious Microsatellite Plugin (RRID:SCR_005466) Copy   

•   Source: SciCrunch Registry

http://blanco.biomol.uci.edu/membrane_proteins_xtal.html

Table providing information about integral membrane proteins whose crystallographic, or sometimes NMR, structures have been determined to a resolution sufficient to identify TM helices of helix-bundle membrane proteins (typically 4 - 4.5 angstroms). It is based upon Preusch et al. (1998) as revised by White & Wimley (1999). Reference is made to all of the protein types whose structures have been determined. They have attempted to make the database as inclusive as possible.

Proper citation: Mpstruct (RRID:SCR_013284) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/cnvhitseq/

A set of Java-based command-line tools for detecting Copy Number Variants (CNVs) using next-generation sequencing data.

Proper citation: cnvHiTSeq (RRID:SCR_013160) Copy   

•   Source: SciCrunch Registry

http://aws.amazon.com/

IT infrastructure services for businesses in the form of web services, now commonly known as cloud computing. This highly reliable, scalable, low-cost infrastructure platform in the cloud powers hundreds of thousands of businesses. With data center locations in the U.S., Europe, Singapore, and Japan, customers across all industries are taking advantage of the following benefits: * Low cost * Agility and Instant Elasticity * Open and Flexible * Secure

Proper citation: Amazon Web Services (RRID:SCR_012854) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/dchipsoft/

Software for analysis and visualization of gene expression and SNP microarrays.

Proper citation: dChip Software (RRID:SCR_013504) Copy   

•   Source: SciCrunch Registry

http://www.russelllab.org/miRNAs/

Data set of 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs.

Proper citation: miRNA (RRID:SCR_010849) Copy   

•   Source: SciCrunch Registry

http://bioinforx.com/lims/online-microarray-gene-expression-data-analysis-software/bxarrays

A web-based microarray data management and microarray analysis system for researchers who need to organize microarray data efficiently and get microarray data analyzed instantly.

Proper citation: BxArrays (RRID:SCR_010971) Copy   

•   Source: SciCrunch Registry

http://genie.weizmann.ac.il/pubs/mir07/mir07_data.html

Catalogs of predicted microRNA targets in worm (based on ce6 genome assembly), fly (dm3), mouse (mm9) and human (hg18). We follow standard seed parameter settings and consider seeds of length 6-8 bases, beginning at position 2 of the microRNA. No mismatches or loops are allowed, but a single G:U wobble is allowed in 7- or 8-mers. In genes missing a 3' UTR annotation, 500 bp (fly), 800 bp (human and mouse) or 300 bp (worm) downstream of the annotated end of the coding sequence were used as the predicted UTR. For each organism, a catalog with zero flank and with a flank of 3 and 15 bases upstream and downstream.

Proper citation: PITA (RRID:SCR_010853) Copy   

•   Source: SciCrunch Registry

http://www-stat.stanford.edu/~tibs/SAM/

Software for genomic expression data mining using a statistical technique for finding significant genes in a set of microarray experiments.

Proper citation: SAM (RRID:SCR_010951) Copy   

•   Source: SciCrunch Registry

http://www.ogt.co.uk/products/246_cytosure_interpret_software

A powerful and easy-to-use software package for the analysis of aCGH data, offering an impressive combination of features.

Proper citation: CytoSure Interpret Software (RRID:SCR_010926) Copy   

•   Source: SciCrunch Registry

http://www.affymetrix.com/estore/browse/level_seven_software_products_only.jsp?productId=131535#1_1

Software that integrates single nucleotide polymorphism (SNP) genotyping, copy number polymorphism (CNP) genotyping, rare copy number variation (CNV) identification, and cytogenetic analyses into one application.

Proper citation: Genotyping Console Software (RRID:SCR_010929) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.vub.ac.be/databases/databases.html

Downloadable data set designed to assess the performance of both multiple and pairwise (protein) sequence alignment algorithms, and is extremely easy to use. Currently, the database contains 2 sets, each consisting of a number of subsets with related sequences. It''s main features are: * Covers the entire known fold space (SCOP classification), with subsets provided by the ASTRAL compendium * All structures have high quality, with 100% resolved residues * Structure alignments have been derived carefully, using both SOFI and CE, and Relaxed Transitive Alignment * At most 25 sequences in each subset to avoid overrepresentation of large folds* Automated running, archiving and scoring of programs through a few Perl scripts The Twilight Zone set is divided into sequence groups that each represent a SCOP fold. All sequences within a group share a pairwise Blast e-value of at least 1, for a theoretical database size of 100 million residues. Sequence similarity is thus very low, between 0-25% identity, and a (traceable) common evolutionary origin cannot be established between most pairs even though their structures are (distantly) similar. This set therefore represents the worst case scenario for sequence alignment, which unfortunately is also the most frequent one, as most related sequences share less than 25% identity. The Superfamilies set consists of groups that each represent a SCOP superfamily, and therefore contain sequences with a (putative) common evolutionary origin. However, they share at most 50% identity, which is still challenging for any sequence alignment algorithm. Frequently, alignments are performed to establish whether or not sequences are related. To benchmark this, a second version of both the Twilight Zone and the Superfamilies set is provided, in which to each alignment problem a number of false positives, i.e. sequences not related to the original set, are added. Database specifications: * Current version: 1.65 (concurrent with PDB, SCOP and ASTRAL) * Twilight Zone set (with false positives): 209 groups, 1740 (3280) sequences, 10667 (44056) related pairs * Superfamilies set (with false positives): 425 groups, 3280 (6526) sequences, 19092 (79095) related pairs

Proper citation: SABmark (RRID:SCR_011817) Copy   

•   Source: SciCrunch Registry

http://bioen-compbio.bioen.illinois.edu/FusionHunter/

Software for identifying fusion transcripts using paired-end RNA-seq.

Proper citation: FusionHunter (RRID:SCR_011895) Copy   

•   Source: SciCrunch Registry

http://www.dnastar.com/t-products-dnastar-lasergene-genomics.aspx

Software for next-gen sequence assembly and analysis in a single, integrated package.

Proper citation: DNASTAR: Lasergene Genomics Suite (RRID:SCR_011854) Copy   

•   Source: SciCrunch Registry

http://www.goldenhelix.com/products/index.html

An integrated collection of user-friendly, yet powerful analytic tools for managing, analyzing, and visualizing multifaceted genomic and phenotypic data.

Proper citation: SNP and Variation Suite (RRID:SCR_011856) Copy   

•   Source: SciCrunch Registry

http://www.jmp.com/software/genomics/

Provides the tools you need to analyze rare and common variants, detect differential expression patterns, discover reliable biomarker profiles, and incorporate pathway information into your analysis workflows.

Proper citation: JMP Genomics (RRID:SCR_011857) Copy   

•   Source: SciCrunch Registry