ANAIS Analysis of NimbleGen Arrays Interface Suite


ANAIS -- a free web-based tool for the processing of NimbleGen expression data.
ANAIS is a user-friendly web-based tool for the processing of NimbleGen expression data. The interface reads single channel microarray files generated by NimbleGen platforms and produces easily interpretable graphical and numerical results. It provides to biologists 6 turnkey analysis modules -normalization, probe to gene, quality controls, differential expression, detection, queries & clustering- to explore quickly, freely and without the need for computer programming, NimbleGen transcriptome data.
The interface is fully described in Simon A, Biot E. (2010). ANAIS: Analysis of NimbleGen Arrays Interface. Bioinformatics 2010 Oct; 26(19):2468-9.

How to use ANAIS
You can input your own NimbleGen files and proceed to :
- Intra and inter-array normalizations
- Summarization of gene expression from probes set
- Quality controls
- Detection analysis to determine which probes or genes are expressed above a threshold based on the random probes
- Differential analysis to determine which probes or genes are statistically differentially expressed among the experimental conditions

Once the analyses steps performed, the web site offers to :
- Perform queries based either on differential expression results, either on gene or probe names, and display the corresponding expression profile plots or clusters
- Download graphs or whole files generated for your project
- Manage your project (download and clear project on the server)

Advices
- The process for data loading can be quite long, depending on the size of data. We appreciate your patience, and we emphasize that ANAIS is dedicated to the analysis of simple experiments and is not designed to handle meta experiments.
- Users are advised to read all the help pages available on the site, often represented by
- IMPORTANT ADVICE (February 2014): Some firefox add-ons extensions seem to be incompatible with ANAIS upload function.
----> If you encounter problems with this function, please disable the extensions as explained here .
----> For french users : aller dans Outils -> Modules complémentaires -> Extensions -> Désactiver tout !



Version : 1.1.0
Last update : 2015 september 21th