TODO.md

In brandonsie/epitopefindr: Minimal Overlaps from BLAST Alignments

allergome 1-100 group 3 has pep 66 multiple

rebuild pkgdown when internet

add annotation files to dropbox phip

push to dev version

debug 1:100

epitopefindr log

--

indexGroups line 135 section still allows merge of duplicated should fix

also some peptides havae NA group, thus fails groupMSA

add progress into to log add job complete to log add newline after pregress bars / remove progress bars when they are done

fix indexgroups algorithm

-- epitoep 88 has 768 splits

make indexgorups faster

alinging groups are always the same. 1 from each?. not necessarily

groups.csv only assigning each peptide ot its last group.

also creates thousands of groups make peptide.once == FALSE by default until ready

try crop out one peptide option

-- make epitopefindr method write.files = TRUE if false, skil MSA skip fwrite in epfind add return of the three spreadsheets epitopekey epitopesummary finalalignments (also initial sequences and starting alignments?) add groups.csv to output? make groupMSA compatible with epitopekey

brandonsie/epitopefindr documentation built on May 4, 2024, 10:27 a.m.