Saulius Lukauskas

[BUG] `LuxSeries.unique` returns incorrect values after subsetting

1

**Describe the bug** `LuxSeries` wrapper around pandas Series, does not compute the unique values correctly for series corresponding to subsets of dataframe. **To Reproduce** Invent some data: ``` data =...

Sample data download link in "Getting started" walkthrough is dead

3

In the "getting started" walkthrough (https://pachterlab.github.io/sleuth_walkthroughs/trapnell/analysis.html) the download link for sample data is broken. Specifically in this code segment ``` wget -O ../Trapnell_results.zip 'https://www.dropbox.com/s/eqx3jmylgns4wd3/Trapnell_results.zip?dl=1' unzip ../Trapnell_results.zip -d .. ``` Link...

`print_help` command is wrong

1

In `dsCompareCurves`, in each line where it says: ``` print_help( opt_parser ) ``` e.g. [here](https://github.com/gtrichard/deepStats/blob/e3685a08db9d10bcb4f1b1742d77bbccfa4656cf/bin/dsCompareCurves#L97) the line should probably say ``` parser$print_help() ``` At least in [`argparse` v2.0.3](https://www.rdocumentation.org/packages/argparse/versions/2.0.3/topics/ArgumentParser) Simple Find...

Redundant rules in linear model

3

The current implementation of `rulefit` can sometimes produce redundant features that are then fed into the lasso. This comes from the stochastic nature of random trees and lack of rule...

No major promoter when internal promoters are strong

2

Hi again, While investigating the `proActiv` results for my sample dataset I came across the fact that many genes do not have a "Major" promoter, yet they tend to have...

Example of how to generate junction file from fastq

1

I realise this is a bit beyond scope for `proActiv` but it would be helpful to have an example on how to generate a valid junction file from raw reads...