Package: alphabetr 0.2.2

alphabetr: Algorithms for High-Throughput Sequencing of Antigen-Specific T Cells

Provides algorithms for frequency-based pairing of alpha-beta T cell receptors.

Authors:Edward Lee [aut, cre]

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alphabetr.pdf |alphabetr.html✨
alphabetr/json (API)

# Install 'alphabetr' in R:
install.packages('alphabetr', repos = c('https://edwardslee.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/edwardslee/alphabetr/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

15 exports 8 stars 1.53 score 20 dependencies 1 mentions 9 scripts 278 downloads

Last updated 8 years agofrom:f8fe7cdc16. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 07 2024
R-4.5-win-x86_64OKSep 07 2024
R-4.5-linux-x86_64OKSep 07 2024
R-4.4-win-x86_64OKSep 07 2024
R-4.4-mac-x86_64OKSep 07 2024
R-4.4-mac-aarch64OKSep 07 2024
R-4.3-win-x86_64OKSep 07 2024
R-4.3-mac-x86_64OKSep 07 2024
R-4.3-mac-aarch64OKSep 07 2024

Exports:bagpipechain_scorescombine_freq_resultscreate_clonescreate_datacreate_data_singlecellsdual_discrim_dual_likelihooddual_discrim_shared_likelihooddual_evaldual_taildual_topfreq_estimatefreq_evallikelihood_singleread_alphabetr

Dependencies:cliclueclusterdplyrfansigenericsgluelifecyclemagrittrmulticoolpillarpkgconfigR6Rcpprlangtibbletidyselectutf8vctrswithr

Using ALPHABETR to determine alpha/beta TCR pairs

Edward S. Lee

Rendered fromalphabetr-vignette.Rmdusingknitr::rmarkdownon Sep 07 2024.

Last update: 2017-01-28
Started: 2016-06-21

Readme and manuals

Help Manual

Help pageTopics
Identify candidate alpha/beta pairs.bagpipe
Calculate association scores between alpha and beta chain pairs.chain_scores
Combines the frequency estimation results from single TCR clones and dual TCR clonescombine_freq_results
Create a synthetic set of clones with a specific underlying clonal structurecreate_clones
Simulate sequencing data obtained from the alphabetr approach with a specified clonal structurecreate_data
Simulate sequencing data obtained single-cell sequencingcreate_data_singlecells
Calculate likelihood of two beta-sharing candidate alpha-beta pairs deriving from a dual clonedual_discrim_dual_likelihood
Calculate likelihood of two beta-sharing candidate alpha-beta pairs deriving from a dual clonedual_discrim_shared_likelihood
Calculate dual depths and false dual rates for simulated alphabetr experimentsdual_eval
Discriminate between beta-sharing clones and dual-alpha TCR clones (optimized for rare clones)dual_tail
Discriminate between beta-sharing clones and dual-alpha TCR clones (optimized for common clones)dual_top
Estimation of frequencies of clones identified by 'alphabetr'freq_estimate
Calculate the precision, CV, and accuracy of frequency estimatesfreq_eval
Calculate likelihood curve of frequency estimates for a dual-alpha or dual-beta TCR clonelikelihood_dual
Calculate likelihood curve of frequency estimates for a dual-alpha and dual-beta TCR clonelikelihood_dualdual
Calculate likelihood curve of frequency estimates for a single TCR clonelikelihood_single
Read in alphabetr sequencing data into the binary matrix form needed by bagpipe()read_alphabetr