Transcriptomics
N.B. This is outside my area of expertise. Please advise about sites to recommend.
DOGMA
DOGMA - is a web
server for proteome and transcriptome quality assessment. The data of
interest are evaluated based on a comparison with a core set of
conserved protein domains and domain arrangements. Depending on the
studied species, DOGMA offers precomputed core sets for different
phylogenetic clades, including Bacteria and Archaea.
(Reference: Kemena C et al. (2019) Nucleic Acids Res 47(W1): W507–W510).
Babelomics 5
Babelomics 5
- offers user-friendly access to a full range of methods that cover:
(i) primary data analysis, (ii) a variety of tests for different
experimental designs and (iii) different enrichment and network
analysis algorithms for the interpretation of the results of such tests
in the proper functional context. Its fifth release includes support
for Next Generation Sequencing data including gene expression
(RNA-seq), exome or genome resequencing.
(Reference: Alonso R et al. (2015) Nucleic Acids Res. 43(W1): W117-221).
ErmineJ
ErmineJ -
performs analyses of gene sets in high-throughput genomics data such as
gene expression profiling studies. A typical goal is to determine
whether particular biological pathways are "doing something interesting"
in an experiment that generates long lists of candidates. The software
is designed to be used by biologists with little or no informatics
background.
(Reference: Gillis J et al. (2010) Nat Protoc. 5(6): 1148-1159).
HPC-T-Annotator
HPC-T-Annotator
- is a tool for de novo transcriptome homology annotation on high
performance computing (HPC) infrastructures, designed for
straightforward configuration via a Web interface. Once the
configuration data are given, the entire parallel computing software
for annotation is automatically generated and can be launched on a
supercomputer using a simple command line. The output data can then be
easily viewed using post-processing utilities in the form of Python
notebooks integrated in the proposed software.
(Reference: Arcioni L et al (2024) BMC Bioinformatics. 25(1): 272).
Cyber-T
Cyber-T - if
you have 2-dye data (such as what would be generated by the usual glass
slide arrays probed with cy3/cy5-labelled cDN) use PAIRED DATA, while
Control+Experimental is for those with Affymetrix-based data consisting
of a separate control and experimental arrays.
(Reference: Kayala, M.A. & Baldi, P. (2012), Nucleic Acids Research, 40 (W1): W553-W559).
NIA Array Analysis Tool
NIA Array Analysis Tool
- for microarray data analysis, which features the false discovery rate
for testing statistical significance and the principal component
analysis using the singular value decomposition method for detecting
the global trends of gene-expression patterns. Additional features
include: analysis of variance with multiple methods for error variance
adjustment, correction of cross-channel correlation for two-color
microarrays, identification of genes specific to each cluster of tissue
samples, biplot of tissues and corresponding tissue-specific genes,
clustering of genes that are correlated with each principal component
(PC), and three-dimensional graphics.
(Reference: A.A. Sharov et al. 2005. Bioinformatics 21: 2548-2549).
TRAPID
TRAPID
- is an online tool for the fast, reliable and user-friendly analysis
of de novo transcriptomes. Through a highly optimized processing
pipeline the TRAPID system offers functional and comparative analyses
for transcriptome data sets. TRAPID is highly competitive with respect
to other existing solutions with regards to both speed and quality.
(Reference: Van Bel M. et al. Genome Biol. 2013;14(12):R134).
TRUFA
TRUFA -
(TRanscriptome User-Friendly Analysis), an open informatics platform
offering a web-based interface that generates the outputs commonly used
in de novo RNA-seq analysis and comparative transcriptomics. TRUFA
provides a comprehensive service that allows performing dynamically raw
read cleaning, transcript assembly, annotation, and expression
quantification. N.B. Requires registration.
(Reference: Kornobis E et al (2015) Evol Bioinform Online 11:97-104).
Chipster
Chipster - is a user-friendly software for analyzing high-throughput data such as NGS and microarrays. It contains over 360 analysis tools and a large collection of reference genomes.
Updated: November, 2025