Transcriptome software tools and databases

Transcriptomics is the study of the transcriptome-the complete set of RNA transcripts that are produced by the genome, under specific circumstances or in a specific cell-using high-throughput methods, such as microarray analysis. Comparison of…

Transcriptomics applications

Most recent bioinformatics tools

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Morning Glory
Dataset

Morning Glory

Provides a database of Japanese morning glory. Morning Glory is an online…

Provides a database of Japanese morning glory. Morning Glory is an online resource of Ipomoea nil or Pharbitis nil, a floricultural plant of Japan. This project collects, develops and distributes…

PHYSCObase
Dataset

PHYSCObase

Provides Physcomitrella patens DNA sequences. PHYSCObase is an online resource…

Provides Physcomitrella patens DNA sequences. PHYSCObase is an online resource that gathers full-length enriched cDNA libraries of P. patens from auxin- and cytokinin-treated gametophytes, as well as…

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QFbase
Dataset

QFbase Macaca fascicularis cDNA database

Provides cDNA sequences derived from the cynomolgus monkey. QFbase is an…

Provides cDNA sequences derived from the cynomolgus monkey. QFbase is an in-house database for the genome data of Macaca fascicularis, the most popular primate species used in biomedical research. It…

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Expression…
Web

Expression Angler

Identifies genes showing similar expression or response profiles from selected…

Identifies genes showing similar expression or response profiles from selected databases. Expression Angler employs the Pearson correlation coefficient to identify co-regulated genes. It provides…

Most popular analytical software and databases

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VENNY
Web

VENNY

Allows comparison of lists with Venn Diagrams. VENNY is a web-server,…

Allows comparison of lists with Venn Diagrams. VENNY is a web-server, consisting in a single standard html file that can be used off-line.

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MiRdup
Desktop

MiRdup

A computational predictor for the identification of the most likely miRNA…

A computational predictor for the identification of the most likely miRNA location within a given pre-miRNA or the validation of a candidate miRNA. MiRdup is based on a random forest classifier…

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Enrichr
Web

Enrichr

An integrative web-based and mobile software application that includes new…

An integrative web-based and mobile software application that includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to…

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Riboswitch…
Web

Riboswitch Scanner

Detects riboswitches from genomic sequences with high sensitivity and…

Detects riboswitches from genomic sequences with high sensitivity and specificity. Riboswitch Scanner uses a method based on profile Hidden Markov Models (pHMMs) for detecting riboswitches.…

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