Vivek Bhardwaj

fix #785

8

closes #785

@dpryan79 so I tried to implement #109 (also related to #86 ) and kind of failed half-way. The option **--NoMeCpG** is a modification of CpG option to ignore the CGC...

methyldackel for GCH context

1

Hi @dpryan79! Would it be easy to implement MethylDackel for GCA, GCC and GCT context (similar to --NOME-seq option for bismark)?

Bonito with modified base rerio model

2

Hello I am trying to call modified all-C context basecalling on our pore R941 data. I tried running bonito with the flipflop rerio model [res_dna_r941_prom_modbases_5mC_v001](https://github.com/nanoporetech/rerio/blob/master/basecall_models/res_dna_r941_prom_modbases_5mC_v001) but can not get it...

add option to install R-devel

2

Thanks for the useful package. I think this would be more complicated than switching to the latest release version but would be useful for package developers who need the devel-version.

new module: sincei

11

Added **sincei** module to summarise read and count-level single-cell QC metrics from [sincei](https://github.com/vivekbhr/sincei) - [x] This comment contains a description of changes (with reason) - [x] `CHANGELOG.md` has been updated...

extract cds sequence +- given bases

1

Hi @gpertea I want to use gffread to get CDS sequences +- N bases. Something like `--w-add ` but for CDS `--x-add `. Would it be easy to implement this?...

testdata for sincei: upcoming module PR

1

Example output from 2 [sincei tools](https://github.com/vivekbhr/sincei) are included: - scFilterStats - scCountQC

Hey Fabian If I don't want the gencode GTF and specify another GTF in `--featureCounts_opts` , it doesn't work. The script still pastes the gencode GTF path while running. featureCounts...

move to .yaml for config?

1

Current config (.ini) file has it's own format, while yaml is a popular and easy to use format. Plus I am not sure if current config allows a hierarchy in...