-
aa-code_3to1.sed
- substitute 3 letter amino acid abbreviations for 1 letter abbrviations -
parse-dssp.sh
- extract secondary structure from PDB files -
exonphaser.sh
- add intron-centric phase to a GFF file -
rebase-gff.pl
- set all intervals in the GFF as offsets from the first interval -
swap_general.sh
- substitute words (with optional pre- and suffixes) using a replacement map -
tozero.pl
- replace things nearly equal to zero with zero
autoslurm.sh
- wraps the given command in a slurm file and runs it
edirect-aliases.sh
gene-code.sh
- print the gene code as a human readable table
lineage2stratum.pl
sciname2taxid.sh
taxid2lineage.pl
taxid2sciname.pl
The following monstrosities should be murdered and replaced with somethig sane.
stratify-seqs.sh
phytable.sh
fasta2blast_taxidmap.sh
round.pl
rplot.R
sumtab.R
summarize-gff.awk
-
entrez-tools
- filters for accessing entrez data -
rentrez-tools
- access entrez tools through an R package. To complete this, just wrap some of the functionality described here, however, it is probably better to just directly use the R package. -
retrieve_uniprot_proteomes.py
- get all proteomes beneath a given common tree node -
sra2srr.sh
- given an SRA id, find the related SRR ids
sync-bib.sh
- recursively extract citations from a tex (or Rnw) file
gff2cds.pl
- use bedtools or bioconductor insteadrename_fasta.sh
- use smof instead