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Dataset . 2023
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ZENODO
Dataset . 2023
License: CC BY
Data sources: Datacite
ZENODO
Dataset . 2023
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Data sources: Datacite
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B-cell receptor data from intratumoural B cells in melanoma patients

Authors: Ng, Joseph;

B-cell receptor data from intratumoural B cells in melanoma patients

Abstract

This record contains data used in the Crescioli et al. analysis of B-cell response in melanoma, specifically analysis concerning high-throughput BCR repertoire. Files: "Visium_all_Aug22_comboDatBoth.txt": IMGT/HighV-Quest output of the high-throughput intratumoural BCR repertoire from n=5 melanoma tumours. In tab-separated text file format. "HV_EB_COV_MEL_comb_Oct22.RDS": A R data object (readable into R with "readRDS(...)") containing combined data from the melanoma (MEL) data with analogous high-throughput BCR repertoire data from healthy volunteers (HV), Ebola convalescent patients (EB) and hospitalised COVID-19 patients (COV). HV, EB and COV data are taken from https://dx.doi.org/10.5281/zenodo.5146019. Here the sequences are filtered to contain only unique combinations of isotype and IMGT-numbered V-domain DNA sequence (to remove redundancies due to e.g. capturing BCR transcripts from plasma cells). "BM_Master_Light_Useasreftrue_140325_withPepStats_8.csv". IMGT/HighV-Quest output of the Bone Marrow light chain repertoire data. Published in Townsend et al. Front Immunol 7:388 (2016). Used here for the comparison of gene conversion frequencies against the melanoma light chain repertoire. "BM_Master_Light_Useasreftrue_140325_withPepStats_8_Vgapped.fasta". The IMGT-gapped V-gene sequence from the Townsend et al. (see above) Bone Marrow light chain repertoire data. This is the raw input to BrepConvert. Provided here for this dataset; same sequences for the melanoma/healthy data are already in the RDS object ("HV_EB_COV_MEL_comb_Oct22.RDS"). "2_IMGT-gapped-nt-sequences_visa.txt", "2_IMGT-gapped-nt-sequences_visb.txt": Raw output of IMGT/HighV-Quest containing IMGT-gapped nucleotide sequences. These files were parsed to extract the IMGT-gapped V-gene sequence for BrepConvert analysis. "BrepConvert.zip": BrepConvert gene conversion analysis results for Healthy and Melanoma repertoires. See code in https://github.com/josef0731/melanoma-ig for ways to use these input files for reproducing the analyses.

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selected citations
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This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
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influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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