Lorena Pantano

Please, go around the documentation and report issues with that or/and offer a PR! link: https://mirtop.readthedocs.io/en/latest/ Thanks!

Add any other tool that could be potentially added. It needs to be maintained at the moment: [X] seqbuster [X] sRNAbench [X] isomiR-SEA [X] Prost [X] miRge [X] BAM file...

support ggplot style figures for stats command

1

Generate a plot like this:  from a file that looks like this: https://github.com/miRTop/mirtop/blob/master/data/examples/plot/example_count.tsv Libraries to use: * https://seaborn.pydata.org/examples/color_palettes.html * https://github.com/yhat/ggpy The code can be added as a script under...

Add an option to convert GFF to VCF pointing to mutations in the sequence. There is code to map from precursor coordinates to genomic coordinates. However the code to get...

Check minimum attributes are there, show possible others to add. Code should be inside `gff/check.py` Here there are multiple examples: https://github.com/miRTop/mirtop/blob/dev/data/examples/gff/*gff `correct_file.gff` should give no warnings, the rest has something...

This will go here somehow: https://github.com/miRTop/mirtop/blob/master/mirtop/mirna/__init__.py#L414

Add column to name the file during `stats` sub-command

1

For that, it has to be implemented code at https://github.com/miRTop/mirtop/blob/dev/mirtop/gff/stats.py#L29. As well, it has to be added one column to indicate the name of the file to be used. By...

The idea is to have an option shared by many functions called `--query`, that allows filtering of the GFF format for: * `Name`, `Variant`, `Filter`, `type` values of the GFF...

Implement DESeq2 like normalization

2

Add the code that from a count matrix, can get the size factor to normalize the data. So, input would be: count data and output: normalized count data. In R...

Plot of isomiRs/miRNA distribution using ggplot-python

8

Implement option in `stats` sub-command like `--detail` to: [ ] show distribution of sequences per sample (geom_density) [ ] boxplot distribution per sample after normalization like DESeq2 [ ] summary...