rtracklayer
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lawremi
R interface to genome annotation files and the UCSC genome browser
Hi, I get an error trying to read gif files using `rtracklayer::import(< gtf file>, format="gtf")`. The same error occurs when I don't specify the format. ``` > library(rtracklayer) > rtracklayer::import("test_file.gtf",...
Hi @lawremi, I am developing a Bioconductor package (m6Aboost) and I meet a windows only bug when I submit the package to bioconductor. The error message looks like this: ```...
http://bioconductor.org/checkResults/release/bioc-LATEST/rtracklayer/tokay1-checksrc.html reflected in https://support.bioconductor.org/p/p133891/
I have a GFF file derived from GeMoMa output. When these GFF files are loaded with `import()`, the following error occurs: ``` Error in .find_start_end_cols ``` I believe the issue...
Hi @lawremi I'm following a GWA tutorial by Reed et al., 2015 and learning how to make regional association plots for candidates SNPs around CETP gene locus. Query "uc002eki.2" and"uc002ekj.2"...
Hi @lawremi I've completed a package named `BiocIO` https://github.com/Bioconductor/BiocIO. The purpose of this package is to migrate high level IO functionality from rtracklayer. This most notably includes the `BiocFile` class...
I am currently performing a RNA-Seq Analysis for Cucumis melo and I am currently trying to load the annotation using makeTxDbFromGFF() from a GFF3 file. When i check the TxDb...
Hi all, Importing a bigwig locally is seemingly failing on windows with the error: ``` x
`rtracklayer` uses [CURLINFO_ACTIVESOCKET](https://curl.se/libcurl/c/CURLINFO_ACTIVESOCKET.html) (Added in curl 7.45.0 ) and [CURLINFO_CONTENT_LENGTH_DOWNLOAD_T](https://curl.se/libcurl/c/CURLINFO_CONTENT_LENGTH_DOWNLOAD_T.html) (Added in curl 7.55.0 ). Centos 7's (EOL was just a month ago) comes with libcurl/7.29.0. Instead of only conditionally...
See https://github.com/lawremi/rtracklayer/issues/123
