Could make it possible to upload our version of FASTA, annotation file, or STRINGdb? I think that the use of your website is quite helpful but most people after using it for screening found at the end that the database is not what they are looking for (e.g. version, species, conversion, etc). For example, regarding the version some have produced their count table based on an older or newer version of the FASTA file. Some others need to use annotation of another species and have the IDs for another organism already converted before uploading but another version again. I think the solution is to allow us to upload our own FASTA, annotation, or STRINGdb, or not sure if it is better for you to connect to the latest 3 versions from a database website without the need for you to download and upload to iDEP? Another point regarding FDR, some people don't work with FDR (padj) but p-values because they don't get any significant FDR. Not all the codes are available to clarify how things worked behind the scenes so that we could modify them if possible if we can't do on iDEP.
Could make it possible to upload our version of FASTA, annotation file, or STRINGdb? I think that the use of your website is quite helpful but most people after using it for screening found at the end that the database is not what they are looking for (e.g. version, species, conversion, etc). For example, regarding the version some have produced their count table based on an older or newer version of the FASTA file. Some others need to use annotation of another species and have the IDs for another organism already converted before uploading but another version again. I think the solution is to allow us to upload our own FASTA, annotation, or STRINGdb, or not sure if it is better for you to connect to the latest 3 versions from a database website without the need for you to download and upload to iDEP? Another point regarding FDR, some people don't work with FDR (padj) but p-values because they don't get any significant FDR. Not all the codes are available to clarify how things worked behind the scenes so that we could modify them if possible if we can't do on iDEP.
Cheers Marwa