Leonardo Collado-Torres

icon indicating a website link http://lcolladotor.github.io icon indicating an email [email protected]

icon company @LieberInstitute icon location Baltimore, USA icon location Find more information about myself at my website where I post my recent publications, talks, blog posts and other updates.

Results 133 comments of Leonardo Collado-Torres

Use devtools::session_info() instead of sessionInfo() for finer information

Awesome =)

Auto completetion of ``` is ` instead of ```

Use the "fenced coded block" command. The shortcut is ctrl + command + c.

Separator (Horizontal Rules) Broken

Both solutions sound good to me =)

Upon the latest update 7.1 of Textmate2 the bundle breaks fonts

Try changing the font at https://github.com/streeter/markdown-redcarpet.tmbundle/blob/master/Preferences/Markup:%20Markdown%20font.tmPreferences#L12 I changed mine from **Helvetica** to **Menlo**.

Upon the latest update 7.1 of Textmate2 the bundle breaks fonts

Nope, no idea

Coverage matrix for regions

Hi, Thank you for your interest in `derfinder`. It sounds like you could use http://lcolladotor.github.io/derfinder/reference/getRegionCoverage.html with `files` specified and `fullCov = NULL`. Best, Leo

HTTP/2 stream 0 was not closed cleanly: INTERNAL_ERROR (err 2)

Hi, I ran into this error from `BiocParallel` as documented at https://github.com/Bioconductor/BiocFileCache/issues/48. Updating my macOS operating system (and command line tools for Xcode) from Ventura 13.4 to 13.5 resolved the...

[Feature Request] Restore information from Matrix Market files in recount3

Hi, It sounds that thanks to Chris we can close this issue. Is that right Jiapei? Best, Leo

recount::getTPM(rse) method

Hm.... http://research.libd.org/recount3/reference/transform_counts.html shows a working case where computing TPMs does work. Also, using your example R code I couldn't reproduce the issue: ```R devel > rse devel > SummarizedExperiment::assays(rse)$counts SummarizedExperiment::assays(rse)$TPM...

recount::getTPM(rse) method

```R devel > rse class: RangedSummarizedExperiment dim: 64837 1048 metadata(8): time_created recount3_version ... annotation recount3_url assays(3): raw_counts counts TPM rownames(64837): ENSG00000278704.1 ENSG00000277400.1 ... ENSG00000182484.15_PAR_Y ENSG00000227159.8_PAR_Y rowData names(10): source type ......