Warren McGee issues

Results 5 issues of


                                            Warren McGee

Feature request: include hdf5 library version as attribute in H5 file and run_info JSON

Hi @pimentel and @pmelsted, The sleuth issues forum has received two separate reports from users that relate to an unexpected incompatibility between the hdf5 library version used in kallisto and...

Speed up sleuth_fit, custom shrinkage function, reconfigure transform API, misc bug fixes

Hi @pimentel, There are a few different things that have been changed here: + significant speed boost in `sleuth_fit` by doing the measurement error and beta covariance calculations with the...

loess uses all computer resources when doing shrinkage

It was discovered during testing that the `loess` function in the standard sleuth shrinkage estimation function (`sleuth:::shrink_df`) is set to use all available cores on the machine in the typical...

`sleuth_gene_table` gives non-sensical results when `gene_mode = TRUE`

Hi @pimentel, This issue just came up on the [forum](https://groups.google.com/d/msg/kallisto-sleuth-users/OpEFdiaJlPU/M43aQBg_AQAJ), where a user was trying to use the `sleuth_gene_table` function with `gene_mode = TRUE`. It is intended for when `gene_mode...

Fix minor bugs in GO-Elite: Mm MPhenoOntology and Hs WikiPathways parsing

Hi, I'm attempting to use the GO-Elite tool, even though it's old, because of its featured ability to handle the issue of gene ontology terms overlapping. In the course of...