Comments (2)
It seems that in this case there should be an error message because chao1 is not suitable for diversity estimation in this case. Do you have any other suggestions on how to deal with it?
from tcr.
Hi, tcR package is no longer supported and current issues will not be fixed. A new package is available that is designed to replace tcR called immunarch. We have solved most of the problems tcR package had and improved the overall pipeline, providing functions for painless repertoire file parsing and publication-ready plot making.
The mission of the immunarch is to make immune repertoire data analysis as easy and possible—even with R. Please feel free to check it here: https://immunarch.com/
If you have any suggestions, bugs, improvements, etc. -- please write us or create an issue in https://github.com/immunomind/immunarch/issues
Thank you! Sincerely,
immunarch dev team and Vadim I. Nazarov, lead developer
from tcr.
Related Issues (20)
- Problem parsing immunoseq for tcR package -- Error: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : scan() expected 'an integer', got 'nodata' HOT 1
- parsing mixcr 3.0.3 file HOT 4
- Error when trying to parse data HOT 1
- Issue with name fixes HOT 1
- tcR conflict with other R packages?
- New immunoSEQ files won't parse. HOT 4
- pca.segments.2D
- plot "vis.gene.usage" by "Read.proportion" HOT 1
- V-segments usage plot only shows fixed 50 V?
- Differential abundance calculation? HOT 1
- Skipping files while parsing HOT 1
- Chao1 tcR
- signif.digits in vis.heatmap does not work as espected HOT 1
- importing mixcr dataset HOT 1
- TRBV6-8 and TRBV6-9 absence form the HUMAN_TRBV set HOT 1
- Names of gene segments in tcR HOT 1
- vis.rarefaction Warning: Ignoring unknown aesthetics: Group HOT 1
- Sample names in mixcr input HOT 1
- Cosine similiarity HOT 1
- Parsing immunoseq data for tcR package
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