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alphabetr (version 0.2.2)

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

Description

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

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Install

install.packages('alphabetr')

Monthly Downloads

383

Version

0.2.2

License

AGPL (>= 3)

Issues

4

Pull Requests

0

Stars

8

Forks

3

Maintainer

Edward Lee

Last Published

January 28th, 2017

Functions in alphabetr (0.2.2)

dual_discrim_shared_likelihood

Calculate likelihood of two beta-sharing candidate alpha-beta pairs deriving from a dual clone
dual_eval

Calculate dual depths and false dual rates for simulated alphabetr experiments
create_data_singlecells

Simulate sequencing data obtained single-cell sequencing
chain_scores

Calculate association scores between alpha and beta chain pairs.
dual_discrim_dual_likelihood

Calculate likelihood of two beta-sharing candidate alpha-beta pairs deriving from a dual clone
combine_freq_results

Combines the frequency estimation results from single TCR clones and dual TCR clones
bagpipe

Identify candidate alpha/beta pairs.
dual_tail

Discriminate between beta-sharing clones and dual-alpha TCR clones (optimized for rare clones)
create_data

Simulate sequencing data obtained from the alphabetr approach with a specified clonal structure
create_clones

Create a synthetic set of clones with a specific underlying clonal structure
freq_eval

Calculate the precision, CV, and accuracy of frequency estimates
likelihood_dual

Calculate likelihood curve of frequency estimates for a dual-alpha or dual-beta TCR clone
freq_estimate

Estimation of frequencies of clones identified by alphabetr
likelihood_dualdual

Calculate likelihood curve of frequency estimates for a dual-alpha and dual-beta TCR clone
dual_top

Discriminate between beta-sharing clones and dual-alpha TCR clones (optimized for common clones)
read_alphabetr

Read in alphabetr sequencing data into the binary matrix form needed by bagpipe()
likelihood_single

Calculate likelihood curve of frequency estimates for a single TCR clone