Sven-Eric Schelhorn

Subset by rownames

1

Hello there, awesome package! It appears as if `fst` currently does not support character rownames, though. For practical and compatibility reasons it would be nice to be able to subset...

Extracting blocks of unaligned reads from CRAM

6

I was wondering if htslib/samtools support extraction of blocks of unaligned reads similar to what a bgzipped FASTQ file that has been indexed with grabix currently allows. This is relevant...

New GDC readout for harmonized TCGA data: 'Allele-specific Copy Number Segment'

2

Hi there, since GDC release 23 there is a new readout for TCGA, 'Allele-specific Copy Number Segment'. It would be great if it were downloadable in TCGAbiolinks via: ```R query.cnv...

Gene fusions

26

Wicked fast indeed! Are there any plans to extend salmon to also detect gene fusion events? There isn't a fast and accurate way to do that yet, only approaches requiring...

Include MTLR model for direct estimation of survival probabilities and supporting feature effects varying over time

2

## Feature Hi there, this is a hugely welcome addition to the R stack for the pharma community! Thanks so much for working on this. Apart from the issues which...

Cufflinks SAM format incompatibility when using STAR-aligned SAM/BAM

7

There seems to be an acknowledged incompatibility of the most recent `cufflinks 2.2.1` that makes it incompatible to certain (standard-compliant) SAM inputs. Specifically, one has to expect the critical `Error...

Feature request: option for getting every nth line

1

It would be great to have an option for getting every `n`th line as well.

Hi Leonardo, thanks for `recount3`; I was wondering whether there is a hack to produce the `RangedSummarizedExperiment` objects using `recount3::create_rse()` for only a subset of samples in a particular SRA...

New model request: gpboost Tree-Boosting with Gaussian Process and Mixed Effects Models

3

The [gpboost](https://cran.r-project.org/web/packages/gpboost/) package on CRAN by @fabsig explains itself as such: > **Combining Tree-Boosting with Gaussian Process and Mixed Effects Models** > An R package that allows for combining tree-boosting...

Great project! In case you are looking for new feature proposals: could we get a summary of the hacker news _comments_ as well, as in the new https://hackyournews.com (which is...