Chenghao (Trevor) Zhu

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

icon company UCLA icon location Los Angeles icon location Postdoctoral Fellow at UCLA JCCC CDS

Results 6 issues of Chenghao (Trevor) Zhu

Best practice for fractionated LFQ

3 comment

Hi, we have a fractionated LFQ sample and we are wondering what's the best practice for processing this data. We currently do this: 1. MZMLSpectrumReindexer (a custom script that makes...

Source Code Availibility for `nfcore_external_java_deps.jar`

6 comment

## Is your feature request related to a problem? Please describe It seems like the [`lib/nfcore_external_java_deps.jar`](https://github.com/nf-core/tools/blob/e0d00d3e09a996f59eb5ce6ebc4795452a5b1d39/nf_core/pipeline-template/lib/nfcore_external_java_deps.jar) compiles groovy code under lib at nextflow runtime. This is really handy. I searched...

question
documentation

Getting genome indices for specific ENSEMBL version

3 comment

We are re-analyzing an cohort of samples done several years ago, and we would like to use the same ENSEMBL/GENCODE version that was used previously. Is there any way to...

help wanted

MSFraggerAdapter doesn't support "cut before amino acd"

1 comment

MSFragger now supports the "cut before amino acid" function since 3.4 (https://github.com/Nesvilab/MSFragger/issues/9), which is not supported by MSFraggerAdapter yet and it will be good to have this added. The parameter...

neoflow_db.nf doesn't allow not outputting reference protein sequences

noeflow_db.nf doesn't allow the `-t` flag of `customProDBJ` which allows not having reference protein sequences being output. I did a quick fix here and am happy to open a PR....

*** buffer overflow detected ***: terminated

7 comment

Hey, I'm having an issue running DIA-NN with an mzML input file converted from Thermo DIA Raw file. I'm using a spectral library generated by DIA-NN with `--gen-spec-lib` (which was...