Raymond Cavalcante

I just wanted to ping this thread and mention that I plan to work on this prior to the next Bioconductor release (October).

Hi, Apologies for the very late reply. I think the lncRNA resource error might have been transient (not dissimilar to Issue #49). I was able to ``` wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/gencode.v19.long_noncoding_RNAs.gtf.gz ```...

All plots will have some constant components: * `GenomeAxisTrack()` * `IdeogramTrack(genome=gen, chromosome=chr)` * We'll need to either pass a genome build to use with `GenomeInfoDb::Seqinfo()`, or make sure to grab...

Something to keep straight in trying to make a general solution is the different usages of `TXID`, `GENEID`, and `TXNAME` in the `TxDb` objects. For instance, in creating a `TxDb`...

Hi, I edited your comment above to make it a bit easier for me to read and locate the pertinent information. What I'm hearing is you ran the same data...

I would like to point out that this is really not a very clear example to try to figure out if a problem exists and what that problem might be....

I think this repository will get to the heart of the matter. https://github.com/rcavalcante/methylsig_comparison I have provided bedGraph files (same format as bismark cov files) in the `bedgraphs` folder. The code...

I will take a look at this in the next few days. I'll also run the data I included in the repo in methylSig v0.4.4. Sorry, I missed that particular...

Hello, I took a look at this in more depth over the weekend and found that the refactor to v0.5.0 caused some changes in the local calculation, which you've already...

Hi, After discussing with the authors, we've decided that we prefer the current approach that methylSig is taking for local information. Namely, that it will only borrow information from loci...