R packages

source: R/README.md

:star: R website

Here is a list of (well, most likely to be difficult to install/update) R packages.

As noted elsewhere, most packages are compiled under gcc/6 – at time of writing this is gcc 6.5.0. Most likely packages will be compiled given C++17, which is furnished with ~/.R/Makevars containing the following lines.

CXX17 = g++ -std=gnu++17 -fPIC

Occasionally, package(s) such as glmnet will indicate this, a practice that facilitates installation greatly.

For completeness, here is the counterpart for biopython

library(Biostrings)
fasta_file_path <- 'https://rest.uniprot.org/uniprotkb/P04217.fasta'
fasta_sequences <- readAAStringSet(fasta_file_path, format = "fasta")
AA_sequence <- fasta_sequences[[1]]
cat("Sequence:", toString(AA_sequence), "\n")
iso_442688365 <- 'TDGEGALSEPSATVTIEELAAPPPPVLMHHGESSQVLHPGNK'
match_position <- regexpr(iso_442688365, AA_sequence)
match_position
mp <- matchPattern(iso_442688365,AA_sequence)
mp

which handles URL and generates more informative output,

> match_position
[1] 186
attr(,"match.length")
[1] 42
attr(,"index.type")
[1] "chars"
attr(,"useBytes")
[1] TRUE
> mp <- matchPattern(iso_442688365,AA_sequence)
> mp
Views on a 495-letter AAString subject
subject: MSMLVVFLLLWGVTWGPVTEAAIFYETQPSLWAESESLLKPLANVTLTCQAHLETPDFQLFKNGVAQEPVHLDSPAIKHQFLLTGDTQGRYRCR...RPQLRATWSGAVLAGRDAVLRCEGPIPDVTFELLREGETKAVKTVRTPGAAANLELIFVGPQHAGNYRCRYRSWVPHTFESELSDPVELLVAES
views:
      start end width
  [1]   186 227    42 [TDGEGALSEPSATVTIEELAAPPPPVLMHHGESSQVLHPGNK]