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https://omictools.com/cross-platform-transcriptome-analysis-tool

Software package for analyzing transcriptome sequencing data from different sequencing platforms.

Proper citation: CPTRA (RRID:SCR_002944) Copy   

•   Source: SciCrunch Registry
  

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

A de novo peptide sequencing algorithm using complementary higher-energy collisional dissociation (HCD) and electron transfer dissociation (ETD) tandem mass spectra.

Proper citation: pNovo+ (RRID:SCR_002860) Copy   

•   Source: SciCrunch Registry
  

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://code.google.com/p/ms-lims/

Software that provides a lightweight, portable yet production-grade solution for managing mass spectrometry based proteomics data.

Proper citation: ms lims (RRID:SCR_002974) Copy   

•   Source: SciCrunch Registry
  

http://hapmap.ncbi.nlm.nih.gov/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A multi-country collaboration among scientists and funding agencies to develop a public resource where genetic similarities and differences in human beings are identified and catalogued. Using this information, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. All of the information generated by the Project will be released into the public domain. Their goal is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. HapMap project related data, software, and documentation include: bulk data on genotypes, frequencies, LD data, phasing data, allocated SNPs, recombination rates and hotspots, SNP assays, Perlegen amplicons, raw data, inferred genotypes, and mitochondrial and chrY haplogroups; Generic Genome Browser software; protocols and information on assay design, genotyping and other protocols used in the project; and documentation of samples/individuals and the XML format used in the project.

Proper citation: International HapMap Project (RRID:SCR_002846) Copy   

•   Source: SciCrunch Registry
  

http://www.ebi.ac.uk/Tools/msa/clustalw2/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. Command line version of multiple sequence alignment program Clustal for DNA or proteins. Alignment is progressive and considers sequence redundancy. No longer being maintained. Please consider using Clustal Omega instead which accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/ClustalW, GCG/MSF, RSF.

Proper citation: Clustal W2 (RRID:SCR_002909) Copy   

•   Source: SciCrunch Registry
  

http://pir.georgetown.edu/pro/

An ontological representation of protein-related entities, explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. PRO encompasses three sub-ontologies: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp).

Proper citation: PRO (RRID:SCR_002902) Copy   

•   Source: SciCrunch Registry
  

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

A software tool to compare two heatmaps and discover patterns within and across groups. In the context of biology, group can be defined based on gene ontology.

Proper citation: pairheatmap (RRID:SCR_003109) Copy   

•   Source: SciCrunch Registry
  

https://github.com/quwubin/MFEprimer/

A fast thermodynamics-based software program for checking PCR primer specificity against genomic DNA and mRNA/cDNA sequence databases.

Proper citation: MFEprimer (RRID:SCR_003066) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/mipe/

A XML format that enables genomics researchers to store critical information on PCR experiments. Accompagnying perl scripts are written to read from (dbSTS) or write to a MIPE XML file.

Proper citation: MIPE (RRID:SCR_003065) Copy   

•   Source: SciCrunch Registry
  

https://github.com/timflutre/eqtlbma/wiki

Software package that implements Bayesian statistical methods to detect eQTLs jointly in multiple subgroups (e.g. tissues). Key features are to borrow information across subgroups, to explicitly model heterogeneity (qualitatively and quantitatively), and to borrow information across genes to estimate hyper-parameters from the data (empirical Bayes).

Proper citation: eQtlBma (RRID:SCR_003102) Copy   

•   Source: SciCrunch Registry
  

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

A software program for reliable multiplex PCR primer design. It employs the widely used primer design program Primer3 and the primer specificity evaluation program MFEprimer to design and evaluate the candidate primers based on genomic or transcript DNA database, followed by careful examination to avoid primer dimerization. The graph-expanding algorithm derived from the greedy algorithm was used to determine the optimal primer set combinations (PSCs) for multiplex PCR. In addition, it provides a virtual electrophotogram to help users choose the best PSC. It is a valuable tool for designing specific, no dimer formation and amplicons size constrained PSCs to improve the multiplex PCR experiments.

Proper citation: MPprimer (RRID:SCR_003063) Copy   

•   Source: SciCrunch Registry
  

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

Software package that provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many canonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.

Proper citation: Triplex (RRID:SCR_003061) Copy   

•   Source: SciCrunch Registry
  

http://www.wormbase.org

Central data repository for nematode biology including complete genomic sequence, gene predictions and orthology assignments from range of related nematodes.Data concerning genetics, genomics and biology of C. elegans and related nematodes. Derived from initial ACeDB database of C. elegans genetic and sequence information, WormBase includes genomic, anatomical and functional information of C. elegans, other Caenorhabditis species and other nematodes. Maintains public FTP site where researchers can find many commonly requested files and datasets, WormBase software and prepackaged databases.

Proper citation: WormBase (RRID:SCR_003098) 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://bioinfo.cipf.es/noiseq/doku.php?id=start

Software used for the identification of differentially expressed genes from count data or previously normalized count data. It empirically models the noise distribution of count changes by contrasting fold-change differences (M) and absolute expression differences (D) for all the features in samples within the same condition. This reference distribution is then used to assess whether the M-D values computed between two conditions for a given gene is likely to be part of the noise or represent a true differential expression.

Proper citation: NOISeq (RRID:SCR_003002) Copy   

•   Source: SciCrunch Registry
  

http://genome.ucsc.edu/cgi-bin/hgPcr?command=start

Tool that searches a sequence database with a pair of PCR primers, using an indexing strategy for fast performance. When successful, the search returns a sequence output file in fasta format containing all sequence in the database that lie between and include the primer pair. The fasta header describes the region in the database and the primers. The fasta body is capitalized in areas where the primer sequence matches the database sequence and in lower-case elsewhere. Sources and executables to run batch jobs on your own server are available free for academic, personal, and non-profit purposes. Non-exclusive commercial licenses are also available.

Proper citation: In-Silico PCR (RRID:SCR_003089) Copy   

•   Source: SciCrunch Registry
  

http://acgt.cs.tau.ac.il/hyden/

Software program for designing pairs of degenerate primers for a given set of DNA sequences. It works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp). It is a batch (i.e., command-line, as opposed to graphical interface) program, available for Windows XP (downloadable version) and Linux (upon request).

Proper citation: HYDEN (RRID:SCR_003126) Copy   

•   Source: SciCrunch Registry
  

http://genes.mit.edu/burgelab/miso/

Probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq and identifies differentially regulated isoforms or exons across samples.

Proper citation: MISO (RRID:SCR_003124) Copy   

•   Source: SciCrunch Registry