Jacob Schreiber

icon indicating a website link https://jmschrei.github.io/ icon indicating an email [email protected]

icon location Research Institute of Molecular Pathology icon location I am a Guest Scientist at the Research Institute of Molecular Pathology in Vienna, studying large scale machine learning and computational biology

Results 259 comments of Jacob Schreiber

[REVIEW]: MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis

@rjorton would you mind generating and filling out the review checklist? Instructions are in the first post.

[REVIEW]: MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis

@editorialbot check references

[REVIEW]: MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis

@editorialbot generate pdf

[REVIEW]: MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis

@mariadelmarq can you please provide a version for the software corresponding to this submission, and a DOI for an archive containing the submission and code, e.g. on Zenodo?

[ENH] Is there utility for single-cell genomics?

I am also interested in this. I'd like to store a single-cell ATAC-seq experiment at basepair resolution. What ended up being the answer?

[ENH] Is there utility for single-cell genomics?

Yes, the idea would be to have a single file flexibly hold a (VERY sparse) cell x genome bp resolution count matrix and be able to access it quickly --...

[ENH] Is there utility for single-cell genomics?

A fragment file is a bed-like file that contains fragments mapped to a reference genome. In addition to the start and end of the reads, it also contains the cell...

[ENH] Is there utility for single-cell genomics?

Ah, interesting, thank you. So you'd be writing one cell and chromosome at a time into it? How long do you think that would take to do? And is there...

[ENH] Is there utility for single-cell genomics?

> Yes, but you could concatenate chromosomes and do the modular arithmetic to know what chrom you are on if you wanted. Sorry, can you elaborate a little here?

[Question] Possible to freeze/constrain specific parameters?

Right now, if you set a HMM transition probability to 0 it will stay 0 forever. As for more general freezing of parameters, even though it would be something conceptually...