Henrietta Holze

ggplotly does not show point size legend for geom_point

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When using ggploty on a geom_point plot the point size legend is not shown. Minimal example to reproduce: ```r library(ggplot2) library(plotly) p

Issues when subsetting and converting loom to seurat

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Hi, I would like to work with the recently published adult human brain atlas which contains 3M cells https://www.biorxiv.org/content/10.1101/2022.10.12.511898v1.full . When I connect to the loom file and want to...

### Description of feature Hi, CNVkit recommends to pool all normal samples, instead of using one matched normal sample for each tumor sample https://cnvkit.readthedocs.io/en/stable/pipeline.html#paired-or-pooled-normals. Could you please implement an option,...

Hi, could you explain how reliable CNVkit is for somatic CNV calling in case of "germline" CNVs? We sequenced a cancer cell line before and after engraftment into mice. I...

10X 5' single-cell data

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Hi @hxj5 , I have a question regarding 10X 5' scRNA-seq data. For 5' sequencing, the read containing cell barcode and UMI contains part of the transcript https://kb.10xgenomics.com/hc/en-us/articles/360000939852-What-is-the-difference-between-Single-Cell-3-and-5-Gene-Expression-libraries. The 10X...

Question on counting overlapping peaks

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Hi, I'm looking at a transcript with a shorter an longer version of an exon. I was wondering how you count reads for those peaks? Like reads that map partially...

umi-tools extract whitelist and count module

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### Name of the tool umi-tools ### Tool homepage https://github.com/CGATOxford/UMI-tools ### Tool description A tool for dealing with UMIs ### Tool output whitelist ``` # UMI-tools version: 1.1.4 # output...

Dear Dr. Sheng Wang, Thank you for maintaining this tool. I am interested in using the property predictions as features in my model. To avoid data leakage in my test...

Question on STRING DB as training data

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Hi Sam, I'm reading up on the tool suite of PPI predictors you developed over the last years. I was wondering on which PPIs exactly you trained (and evaluated) D-SCRIPT,...