Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
http://sourceforge.net/projects/cnvcapseq/
Software for accurate and sensitive CNV discovery and genotyping in long-range targeted resequencing.
Proper citation: cnvCapSeq (RRID:SCR_012126) Copy
http://sourceforge.net/projects/ealps/
Software that uses the genotype data in conjunction with the pooled sequence data in order to accurately estimate the proportions of the samples in the pool, even in cases where not all individuals in the pool were genotyped (eALPS-LD).
Proper citation: eALPS (RRID:SCR_012130) Copy
http://sourceforge.net/projects/plek/
An alignment-free software tool which uses a computational pipeline based on an improved k-mer scheme and a support vector machine (SVM) algorithm to distinguish lncRNAs from messenger RNAs (mRNAs), in the absence of genomic sequences or annotations. It is especially suitable for PacBio or 454 sequencing data and large-scale transcriptome data.
Proper citation: PLEK (RRID:SCR_012132) Copy
http://sourceforge.net/projects/ldx/
A computational software tool for estimating linkage disequilibrium (LD) from pooled resequencing data.
Proper citation: LDx (RRID:SCR_012131) Copy
http://pprospector.sourceforge.net/
A pipeline of software programs to design and analyze PCR primers. It is built in Python using the open-source PyCogent toolkit.
Proper citation: PrimerProspector (RRID:SCR_012136) Copy
http://musite.sourceforge.net/
A Java-based standalone application for predicting both general and kinase-specific protein phosphorylation sites.
Proper citation: Musite (RRID:SCR_012141) Copy
http://sourceforge.net/projects/phosphosite/
A bioinformatical software tool for analyzing (quantitative) phosphoproteome datasets. The program retrieves kinase-substrate predictions from NetworKIN and contains various statistical modules for futher analysis.
Proper citation: PhosphoSiteAnalyzer (RRID:SCR_012142) Copy
http://sourceforge.net/projects/cnv/
Software for a web-enabled platform for analyzing genome variation such as copy number variation (CNV).
Proper citation: CNV Workshop (RRID:SCR_012635) Copy
http://sourceforge.net/p/krona/home/krona/
Software that allows hierarchical data to be explored with zoomable pie charts.
Proper citation: Krona (RRID:SCR_012785) Copy
http://seqpig.sourceforge.net/
A software library for Apache Pig for the distributed analysis of large sequencing datasets on Hadoop clusters.
Proper citation: SeqPig (RRID:SCR_008548) Copy
http://geckoe.sourceforge.net/
A complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community.
Proper citation: Gecko (RRID:SCR_009001) Copy
http://scalce.sourceforge.net/Home
A FASTQ compression tool that uses locally consistent parsing to obtain better compression rate.
Proper citation: SCALCE (RRID:SCR_009658) Copy
http://sourceforge.net/projects/taipan/
A fast hybrid short-read assembly tool.
Proper citation: Taipan (RRID:SCR_007330) Copy
http://genotan.sourceforge.net/
A free software tool to identify length variation of microsatellites from short sequence reads.
Proper citation: GenoTan (RRID:SCR_007935) Copy
A cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.
Proper citation: BRIG (RRID:SCR_007802) Copy
http://sourceforge.net/projects/fas-dpd/
Software program to design degenerate primers for PCR.
Proper citation: FAS-DPD (RRID:SCR_003068) Copy
http://sourceforge.net/projects/salt1/
Software that can accurately and sensitivity classify short reads of next-generation sequencing (NGS) into protein domain families. It is based on profile HMM and a supervised graph contribution algorithm. Compared to existing tools, it has high sensitivity and specificity in classifying short reads into their native domain families.
Proper citation: SALT (RRID:SCR_003187) Copy
http://sourceforge.net/projects/xorro-overlap/
Efficient paired-read overlap software program for use with Illumina sequencing.
Proper citation: XORRO (RRID:SCR_003181) Copy
http://compbio.cs.sfu.ca/software-novelseq
Software pipeline to detect novel sequence insertions using high throughput paired-end whole genome sequencing data.
Proper citation: NovelSeq (RRID:SCR_003136) Copy
http://mrcanavar.sourceforge.net/
Copy number caller that analyzes the whole-genome next-generation sequence mapping read depth to discover large segmental duplications and deletions. It also has the capability of predicting absolute copy numbers of genomic intervals.
Proper citation: mrCaNaVaR (RRID:SCR_003135) Copy
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the nidm-terms Resources search. From here you can search through a compilation of resources used by nidm-terms and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that nidm-terms has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on nidm-terms then you can log in from here to get additional features in nidm-terms such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
You can save any searches you perform for quick access to later from here.
We recognized your search term and included synonyms and inferred terms along side your term to help get the data you are looking for.
If you are logged into nidm-terms you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the sources that were queried against in your search that you can investigate further.
Here are the categories present within nidm-terms that you can filter your data on
Here are the subcategories present within this category that you can filter your data on
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
