Anna James-Bott

UMI extraction 3' end

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Hi, Fastp is a great tool! I was wondering if it's possible to extract UMIs from both the 5' and 3' end of a fastq. Is there an option to...

plotFingerprint bigwig support

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Hello, I was wondering if plotFingerprint supports bigwig input files? The documentation mentions using bigwigs or indexed BAM files as input: https://deeptools.readthedocs.io/en/develop/content/tools/plotFingerprint.html (_plotFingerprint randomly samples genome regions (bins) of a...

Accompanying bash commands

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Hello, I was wondering if you have example command line commands or bash scripts you used for preprocessing with Kallisto bustools. Thanks! Best, Anna

All the other packages I'm using require numpy >= 2. Any chance of support for numpy version 2?

Hello, I'm trying to get curated ligand and receptor pairs. Currently I'm running: ``` library(OmnipathR) library(tidyverse) lr = curated_ligand_receptor_interactions( curated_resources = c("Guide2Pharma", "HPMR", "ICELLNET", "Kirouac2010", "CellTalkDB", "CellChatDB", "connectomeDB2020"), cellphonedb =...