sofia

interpretation rankNet mode comparison and netAnalysis_signalingRole_heatmap

3

Hello, I am having troubles to interpretate the output from rankNet(cellchat, mode = "comparison", stacked = T, do.stat = TRUE)$data. I am attaching a pdf file to explain my workflow....

Using marker genes with different length

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Hello, thanks for developing this package. I am trying to compare my clusters with the clusters of a previously published scRNA seq dataset. The reference clusters don't have the same...

AnnotateBamWithUmis, sorted or unsorted BAMs? code example?

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Dear fgbio team, I would like to use AnnotateBamWithUmis, however I am not very sure about the steps to take. I couldn't find any tutorial that refers to AnnotateBamWithUmis. I...

No adapter detected for read2 and Insert size peak (evaluated by paired-end reads): 103

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Hello! Thanks for the great software. I am running fastp for paired end reads obtained from an Illumina machine, and feeding it with a list of adaptors. It worked good...

Different adaptors detected in paired reads

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Hi, may I ask if it is normal (correct) to detect different adaptors sequence in the paired reads? (attached a picture with the example) Thanks for your help! [fastp.pdf](https://github.com/OpenGene/fastp/files/11868397/fastp.pdf)

Hi, Thanks for your great package. I have paired end RNA seq data, with three fastq files per samples. I used Hisat2 to align R1 and R2 reads, and then...

se.read_maxwell error: "Unable to synchronously open object (object 'rec0001' doesn't exist)"

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Hello, I'm currently working with spikeinterface using Maxwell data. While I haven't encountered any issues reading MaxOnw data, I'm facing a problem with MaxTwo data. My objective is to read...

Hi, I really want to try this package, but unfortunately I haven't been able to install it. I tried on a centos machine and an ubuntu machine, but in both...

MAGMA.Celltyping::import_magma_files issue

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## 1. Bug description I was previously using the following code to extract the GWAS summaries of **1)** Biological insights from 108 schizophrenia-associated genetic loci. Nature, 2014 **2)** Genome-wide association...

error when using .merge(pairs)

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Hi, I have been using the function scur.get_potential_auto_merge() to get pairs f neurons to be merged and then I merge them with .merge(pairs). It works well most of the time,...