LuisHeinzlmeier

Add UMI bias figure

1

This is only a small PR adding a figure to the `raw_data_processing` chapter.

Adding tables + improve structure of strengths and limitations

1

Adding tables to compare the benefits and limitations of "Sequencing generations" and "Single-cell sequencing protocols". This would make it easier for the reader to compare differences. Maybe shorten the first...

Create a style guide explaining how we want to structure our chapters.

Some chapters did not have their own yml file or no yml files. No yml file at all: - air repertoire - deconvolution Only one yml file for a whole...

File format chapter

1

An own chapter on file formats, which shows and explains the most important file formats.

Create a figure for UMI resolution (https://www.sc-best-practices.org/introduction/raw_data_processing.html#umi-resolution). Something like this (https://www.ecseq.com/support/ngs/how-can-unique-molecular-identifiers-help-to-reduce-quantitative-biases). Maybe also include common problems like "Errors in UMIs", "Multimapping", “convergent”, and “divergent” UMI collisions.

Update data types (hasheddrops)

2

- updated data types for the parameters so that we can use them in the hadge pipeline

- added correct version of used packages - updated data types for the used parameters that we can use it in the hadge pipeline - updated to Harshil Alignment™️ format

- updated to Harshil Alignment™️ format - updated data types for the parameters so that we can use them in the hadge pipeline

Bff

7

- Generating cell hashing calls from a matrix of count data by calling `GenerateCellHashingCalls` - This modules was created to be included in the `hadge` pipeline - Currently the module...