testthat, entropy, proxy, knitr, rmarkdown

Minimal Protein Set Explaining Peptide Spectrum Matches
Determine minimal protein set explaining peptide spectrum matches.

Minimal Protein Set Explaining Peptide Precursors
Determine minimal protein set explaining peptide precursors.

Determine minimal protein set explaining
peptide spectrum matches. Utility functions for creating fasta amino acid databases with decoys and contaminants.
Peptide false discovery rate estimation for target decoy search results on psm, precursor, peptide and protein
level.
AhoCorasickTrie, Matrix, doParallel, foreach, plyr, readr,
seqinr, stringr, dplyr

Determine minimal protein set explaining
peptide spectrum matches. Utility functions for creating libraries with decoys.
Planned is peptide FDR estimation for search results.
AhoCorasickTrie, Matrix, doParallel, foreach, plyr, seqinr,
stringr

c(person("Witold", "Wolski",
email = c("wewolski@gmail.com"),
role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-6468-120X")))
Determine minimal protein set explaining
peptide spectrum matches. Utility functions for creating fasta amino acid databases with decoys and contaminants.
Peptide false discovery rate estimation for target decoy search results on psm, precursor, peptide and protein
level. Computing dynamic swath window sizes based on MS1 or MS2 signal distributions.
AhoCorasickTrie, docopt, Matrix, methods, purrr, readr, rlang,
seqinr, stringr, dplyr
'annotatePeptides.R' 'readjustWindow.R' 'cdsw.R'
'computeFDR.R' 'createDecoyDB.R' 'create_fgcz_fasta_db.R'
'greedy.R' 'hello.R' 'loadContaminantsFasta.R'
'prepareMatrix.R' 'readFasta.R' 'removeSignalPeptides.R'
'reverseSeq.R' 'writeFasta.R' 'zzz.R'
Witold Wolski [aut, cre] (<https://orcid.org/0000-0002-6468-120X>)

Reverse depends for a given package are queued such that multiple
workers can run the tests in parallel.
config, liteq, data.table, crayon, DBI, RSQLite

Tabular Data Backed by Partitioned 'fst' Files
c(person(given = "Nicolas",
family = "Bennett",
role = c("aut", "cre"),
email = "nicolas.bennett@stat.math.ethz.ch"),
person(given = "Drago",
family = "Plecko",
role = "ctb",
email = "drago.plecko@stat.math.ethz.ch"))
Intended for larger-than-memory tabular data, 'prt' objects provide an interface to read row and/or column subsets into memory as data.table objects. Data queries, constructed as 'R' expressions, are evaluated using the non-standard evaluation framework provided by 'rlang' and file-backing is powered by the fast and efficient 'fst' package.
assertthat, fst, data.table, utils, vctrs, tibble, cli,
pillar, crayon, fansi, backports, rlang, knitr
testthat, xml2, covr, withr, nycflights13, datasets,
rmarkdown, bench
Nicolas Bennett [aut, cre],
Drago Plecko [ctb]