Harold Pimentel

Give helpful error message when no reads align

1

Currently, we do not check at the end of a run if no reads aligned. As a result, some people have been getting 0 reads mapping and 'nan' everywhere in...

Issue reading h5 files

74

Some users have reported having issues reading the H5 files. Here is the error: ``` > so

Reduce dependencies

1

The dependencies are kind of insane for new R users and can take quite some time from a fresh R install. We should try to clean this up a snuck...

deal with suffix id in ensembl transcriptomes

4

It seems that ensembl appends '.X' to the transcript id denoting the version of that transcript. http://sites.tufts.edu/cbi/files/2013/01/Introduction2ENSEMBL.pdf https://www.biostars.org/p/102769/ When there is a `target_mapping` provided and the intersection between the transcript...

Report a better error when design matrix is singular

11

Error message is pretty hopeless if you don't know what's happening under the hood: ``` Error in solve.default(t(X) %*% X) : Lapack routine dgesv: system is exactly singular: U[5,5] =...

NA in likelihood ratio test

6

look into why we are getting `NA` in `sleuth_lrt()` and look into what `p.adjust` is doing in this situation (treating them as ones?)

number of bootstraps not showing in `devel`

2

With Pascal's new version we are getting bootstrap == 0. We should basically populate this when reading the bootstraps.

merge back in documentation to `sleuth_live`

1

somehow in the merge the documentation (hovering over things) was removed.

I am sure there are more things that don't have download buttons. We should look carefully and fix all of these before the next release.

Read GTF and get trans=> gene mapping

2

There is probably some way to do this in general for any annotation in BioConductor. It is easy to do using `biomaRt` for Ensembl, but that's insufficient. It's probably best...