immunarch

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Warning in Reading 10X data

1

To all, I just load the TCR data from 10X using repLoad, but the warning massage returns; Warning message: The following named parsers don't match the column names: barcode,is_cell,contig_id,high_confidence,length,chain,v_gene,d_gene,j_gene,c_gene,full_length,productive,cdr3,cdr3_nt,reads,umis,raw_clonotype_id,raw_consensus_id This...

HocheolJang426

Loading 10X V(D)J data

2

Hey, I am using cellranger version 7.0 and running the `cellranger vdj` function. The output of `cellranger vdj` function contains a folder named `outs` (as described here [https://support.10xgenomics.com/single-cell-vdj/software/pipelines/7.0/tutorial/tutorial-vdj](url)). I am...

barakt123

repDiversity -raref Error

6

Dear all, I am getting an error while using the repDiversity function with method set to raref, the issue is the same as https://github.com/immunomind/immunarch/issues/19, however I don't understand how to...

AimSchina

support for TRUST4 output

12

Hello, Is there a way that I can load data output from TRUST4 into Immunarch? Thanks, Nadia

natallah

Suggestions

2

Hi ImmunoMind team, Thank you so much for such a great tool as immunarch. I tried it for my analysis and I have suggestions for possible improvements: - Design part:...

teresho4

Failed to install 'immunarch' from GitHub

1

I am trying to install immunarch from Github: `devtools::install_github("immunomind/immunarch", ref="master")` But I get the error: ``` Error: Failed to install 'immunarch' from GitHub: (converted from warning) installation of package ‘/var/folders/tp/8lzvqv3s6nj5cfw_623lz42r0000gq/T//Rtmper7Frl/file11161e7eb4d8/immunarch_0.6.7.tar.gz’...

anabbi

trackClonotypes ordering of clonotypes feature?

1

Is it possible to choose the order in which the clonotypes are displayed in the stacked bar chart when visualizing the trackClonotypes data? The default is alphabetical and I can't...

tdm76

geneUsageAnalysis: Can't convert from <double> to <integer> due to loss of precision.

2

Hello, I tried to do gene usage analysis using TRBV: `imm_gu

anabbi

Problem with `filter()` input `..1`

2

## ❓ Questions and Help When I try to analyze my data with any of the available functions e.g.: > exp_vol

kalinabelcheva

repExplore question

1

Hey, I am trying to visuilize (as a pie chart for example) the clonal expansion within each sample. Can I get a similar output to the RepEpxplore() function but instead...

christoforos-dimitropoulos