Abolfazl (Abe)

Dataverse data access module

7

### Aim Including a draft [dataverse](https://dataverse.harvard.edu/) data collector as part of `gget` tool boxes. e.g. ```bash gget dataverse -j dataverse.json -o path-to-dir ``` ### Tasks - [x] make a python...

### Request type Extension of existing module ### Request description I tried to use `gget blast` and I noticed I can not filter by taxonomy. It would be nice if...

Using kite for haircut-seq

1

Dear Pachter Lab members, There is a single-cell method named [haircut-seq](https://academic.oup.com/nar/article/doi/10.1093/nar/gkaa240/5819935) which I'm trying to reimplement their pipeline using kallisto | bustools. I found _kite_ the right tool for this...

Switch size factor analysis to pyDESeq2

2

[Here](https://www.sc-best-practices.org/preprocessing_visualization/normalization.html#shifted-logarithm) there is a size factor calculation in R which can be painful (i.e. setting up stable environment, etc.) ! I would use pyDESeq2 since it's now a well maintained...

merge paired-end sequences

5

**merge-paired-end-sequences** - https://github.com/dstreett/FLASH2 - https://cme.h-its.org/exelixis/web/software/pear/ - https://micca.readthedocs.io/en/1.6.2/pairedend.html#merge-paired-end-sequences - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5657622/ _Originally posted by @abearab in https://github.com/wheretrue/biobear/issues/102#issuecomment-1968053646_

alternative for `seqkit locate` that can locate subsequences/motifs

12

I found [seqkit locate](https://bioinf.shenwei.me/seqkit/usage/#locate) very useful but it was surprisingly slow. Would you think there is any `biobear` approach for that? In general, any seqkit functions are very common and...

How to run polars dataframe methods on large FASTQ files in a memory efficient way

5

As I mentioned in [this comment](https://github.com/wheretrue/biobear/issues/96#issuecomment-1965529578), I'm interested in applying "groupby" function on polars dataframe. My goal is counting all unique sequences in a FASTQ file. I have a few...

Support guide efficiency prediction for DjCas13d [feature request]

1

It would be nice if crisprVerse can support DjCas13d! > Wei, J., Lotfy, P., Faizi, K., Baungaard, S., Gibson, E., Wang, E., Slabodkin, H., Kinnaman, E., Chandrasekaran, S., Kitano, H.,...

Design spacer for CRISPR-Csm transcript targeting systems [feature request]

2

Are you adding any features for CRISPR-Csm transcript targeting systems? https://www.nature.com/articles/s41587-022-01649-9

Alignments error while using `PairedGuideSet` object as input

2

Is it possible to run `addSpacerAlignmentsIterative` on `PairedGuideSet` object?! I an error running this code: ```R pairsGuideSet