frenkiboy

Add the new randomization algorithm which keeps the distribution of feature and interfeature distances

Annotation of genomic features object

2

Maybe our function should work also with genomic features objects?

The Aggregate function crashes with a cryptic subset error when the above condition is not satisfied. I thought it would create an invalid SingleCellExperiment object, but it doesn't. Happens often...

documentation for development

1

A detailed documentation for development which will track the most recent changes - i.e. when a .in file appears, that we know where it is used, and why, and that...

refactoring .in files

2

Develop a system without the .in files - i.e. have a local config/settings file which would define which filea need to be changed during the configuration steps (which would also...

Ignore .Renviron

1

The pipeline reads the .Renviron files in the current directory. This can mess up R dependencies.

multiqc dies with large number of samples

5

We used the pipeline for the analysis of ~300 smart seq samples. multiqc died with the following error: raceback (most recent call last): File "/gnu/store/crsh6vl6a2pwiad9a9vcd7gyq0wp83xi-multiqc-1.5/bin/.multiqc-real", line 767, in multiqc() File...

The pipeline should be easily extendable for one or more types of splicing analysis. 1. VAST tools 2. MAJIQ 3. IsoformSwitchAnalyzerR

numbered sections

1

Is it possible to have numbered sections as in normal markdown documents? i.e. by setting number_sections under render?