TRANSCRIPTOMICS
N.B. This is outside my area of expertise. please advise about sites to recommend

 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 - 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. Iits fifth release, which 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 - 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 - 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 -  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 - 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 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 (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 - 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: August, 2025