Tools   Select Another Resource Report Type

http://plntfdb.bio.uni-potsdam.de

Public database arising from efforts to identify and catalogue all plant genes involved in transcriptional control.Integrative plant transcription factor database that provides web interface to access large sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana (thale cress), Populus trichocarpa (poplar), Oryza sativa (rice), Chlamydomonas reinhardtii and Ostreococcus tauri. Provides access point to its daughter databases of species-centered representation of transcription factors (OstreoTFDB, ChlamyTFDB, ArabTFDB, PoplarTFDB and RiceTFDB). Information including protein sequences, coding regions, genomic sequences, expressed sequence tags, domain architecture and scientific literature is provided for each family.

Proper citation: PlnTFDB (RRID:SCR_010899) Copy   

•   Source: SciCrunch Registry
  

http://www.beaumont.ie/

Hospital in Dublin.

Proper citation: Beaumont Hospital; Dublin; Ireland (RRID:SCR_011070) Copy   

•   Source: SciCrunch Registry
  

http://www.stat.wisc.edu/~keles/Software/mosaics/

Software developed as a flexible mixture modeling approach for detecting peaks of one-sample (ChIP sample) or two-sample (ChIP sample and matched control sample) ChIP-seq data.

Proper citation: MOSAiCS (RRID:SCR_010861) Copy   

•   Source: SciCrunch Registry
  

https://www.meliordiscovery.com/

Provider of in vivo pharmacology services.Pioneer of in vivo phenotypic screening and leader in area of drug repositioning. Its proprietary theraTRACE platform enables identification of new therapeutic potential by systematically screening candidates in diverse array of validated in vivo disease models.

Proper citation: Melior Discovery (RRID:SCR_010986) Copy   

•   Source: SciCrunch Registry
  

http://sissrs.rajajothi.com/

Anl algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments.

Proper citation: SISSRs (RRID:SCR_010866) Copy   

•   Source: SciCrunch Registry
  

http://bioinfo.au.tsinghua.edu.cn/software/NURD/

An algorithm to inference isoform expression., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: NURD (RRID:SCR_010988) Copy   

•   Source: SciCrunch Registry
  

http://code.google.com/p/zinba/

Software to identify genomic regions enriched in a variety of ChIP-seq and related next-generation sequencing experiments (DNA-seq), calling both broad and narrow modes of enrichment across a range of signal-to-noise ratios. ZINBA models and accounts for factors that co-vary with background or experimental signal, such as G/C content, and identifies enrichment in genomes with complex local copy number variations. ZINBA provides a single unified framework for analyzing DNA-seq experiments in challenging genomic contexts.

Proper citation: ZINBA (RRID:SCR_010868) Copy   

•   Source: SciCrunch Registry
  

http://archive.igbmc.fr/recherche/Prog_FGC/Eq_HGron/Polyphemus.html

R package for comparative analysis of RNA Polymerase II ChIP-Seq profiles by non-linear normalization.

Proper citation: POLYPHEMUS (RRID:SCR_010870) Copy   

•   Source: SciCrunch Registry
  

https://wyzerbio.com/wyzerBioWebapp/

Full service DNA sequencing and DNA prep provider founded in 2011, located at 85 Bolton Street in Cambridge, MA.

Proper citation: Wyzer Biosciences Inc. (RRID:SCR_010991) Copy   

•   Source: SciCrunch Registry
  

http://code.google.com/p/diffreps/

Finding differential chromatin modification sites from ChIP-seq data.

Proper citation: diffReps (RRID:SCR_010873) Copy   

•   Source: SciCrunch Registry
  

http://www.webcitation.org/getfile?fileid=c6d148fcb4fde0ea6991ec319a7a3925d38f32bf

A software program which finds sequence elements conserved in a set of DNA sequences.

Proper citation: AlignACE (RRID:SCR_010875) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/p/arpeggio/wiki/Home/

Software for harmonic compression of ChIP-seq data reveals protein-chromatin interaction signatures.

Proper citation: Arpeggio (RRID:SCR_010876) Copy   

•   Source: SciCrunch Registry
  

http://autosome.ru/dichipmunk/

Software for motif discovery using dinucleotide position weight matrices (PWMs).

Proper citation: diChIPMunk (RRID:SCR_010879) Copy   

•   Source: SciCrunch Registry
  

http://www.neuroservice.com

Private Contract Research Organization providing pharmacological assays based on electrophysiological recordings of acute brain slices, spinal cord slices, cultured neurons, human brain slices and iPSC-derived neurons. These assays are performed with two complementary techniques: Multi-Electrode Array (MEA) and Patch-Clamp.

Proper citation: NEUROSERVICE (RRID:SCR_011053) Copy   

•   Source: SciCrunch Registry
  

http://www.scienceexchange.com/facilities/mobileworks

THIS RESOURCE IS OUT OF SERVICE, documented on February 3rd,2022. Experiments generate millions of datapoints, hours of video, or terabytes of images. Manually coding or classifying large datasets can require thousands of hours of time that are better spent elsewhere. MobileWorks uses a crowd of thousands of trained individuals worldwide to carry out accurate data classification, labeling, and coding on demand. We can process images, audio and video data reliably according to your criteria. We use strict filtering and testing algorithms to verify that your labeling processes are followed precisely. Each label is produced through agreement by two or more individuals working in parallel and algorithmically verified.

Proper citation: MobileWorks (RRID:SCR_011056) Copy   

•   Source: SciCrunch Registry
  

http://kmersvm.beerlab.org/

A webserver built on the Galaxy framework that enables the mining of sequence data for transcription factor binding sites. This tool suite was designed to aid in analysis of next-generation sequencing (NGS) data that uses a support vector machine (SVM) with kmer sequence features to identify predictive combinations of short transcription factor binding sites which determine the tissue specificity of the original NGS assay. While you may use datasets already available from Galaxy, you can upload your data using the ''Get Data'' Tool. The tool can upload data from a variety of locations.

Proper citation: kmer-SVM (RRID:SCR_010882) Copy   

•   Source: SciCrunch Registry
  

http://www.rennes.inra.fr/en

Research center

Proper citation: INRA Rennes (RRID:SCR_011300) Copy   

•   Source: SciCrunch Registry
  

http://www.ibioinformatics.org/

The Institute of Bioinformatics and Applied Biotechnology (IBAB) is a non-profit autonomous institute set up by the Department of IT, BT and S and T, Government of Karnataka. It is located in a 20-acre campus in the southern part of the City of Bengaluru and is a part of Biotech Park.

Proper citation: Institute of Bioinformatics; Bangalore; India (RRID:SCR_011306) Copy   

•   Source: SciCrunch Registry
  

http://www.helmholtz-muenchen.de/en/ibis

Hosts the Munich Information Center for Protein Sequences (MIPS) and its main focus is the genome-oriented bioinformatics, in particular the systematic analysis of genome information including the development and application of bioinformatics methods in genome annotation, expression analysis and proteomics. MIPS supports and maintains a set of generic databases as well as the systematic comparative analysis of microbial, fungal, and plant genomes.

Proper citation: Institute of Bioinformatics and Systems Biology; Neuherberg; Germany (RRID:SCR_011307) Copy   

•   Source: SciCrunch Registry
  

http://www.cnrs.fr/insb/

The Institute of Biological Sciences (INSB) is a CNRS institute that develops and coordinates research in biological sciences with the overall aim to better understand life in all its complexity, starting at the level of atoms and biomolecules, extending to cells and through to organisms and populations. Scientific fields: structural biology, bioinformatics, pharmacology, neuroscience, cognitive science, immunology, genetics, cell biology, microbiology, physiology, plant biology, systems biology, biodiversity...

Proper citation: Institute of Biological Sciences (RRID:SCR_011308) Copy   

•   Source: SciCrunch Registry