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https://www.infoquant.com/cghfusion

Software for DNA Copy Number and loss of heterozygosity (LOH) analysis designed with high-throughput diagnostic laboratories in mind.

Proper citation: CGH Fusion (RRID:SCR_000295) Copy   

•   Source: SciCrunch Registry

https://github.com/hmsiccbl/screensaver

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for a Lab Information Management System (LIMS) for high-throughput screening of small molecule and RNAi biological assays.

Proper citation: Screensaver (RRID:SCR_000297) Copy   

•   Source: SciCrunch Registry

http://anya.igsb.anl.gov/Geneways/GeneWays.html

System for automatically extracting, analzying, visualizing and integrating molecular pathway data from the research literature. System focuses on interactions between molecular substances and actions, providing a graphical consensus view on the collected information. GeneWays is designed as open platform, allowing researchers to query, review and critique integrated information.

Proper citation: GeneWays (RRID:SCR_000572) Copy   

•   Source: SciCrunch Registry

http://bowtie-bio.sourceforge.net/recount/

RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward.

Proper citation: ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) Copy   

•   Source: SciCrunch Registry

http://www.bioinfor.com/zoom/general/overview.html

Software to map the Illumina/Solexa reads of 15x coverage of a human genome to the reference human genome in one CPU-day, allowing two mismatches, at full sensitivity.

Proper citation: ZOOM (RRID:SCR_002175) 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

http://www.partek.com/?q=partekgs

A comprehensive suite of advanced statistics and interactive data visualization specifically designed to reliably extract biological signals from noisy data.

Proper citation: Partek Genomics Suite (RRID:SCR_011860) Copy   

•   Source: SciCrunch Registry

http://sbcb.bioch.ox.ac.uk/cgdb/

A database of membrane protein/lipid interactions by coarse-grained molecular dynamics simulations.

Proper citation: CGDB (RRID:SCR_011959) Copy   

•   Source: SciCrunch Registry