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config
config
 
 
experimental
experimental
 
 
filetracker
filetracker
 
 
helper
helper
 
 
include
include
 
 
remote
remote
 
 
tests
tests
 
 
.gitignore
.gitignore
 
 
.gitmodules
.gitmodules
 
 
COPYING
COPYING
 
 
README.textile
README.textile
 
 
analyze-protein-groups.rb
analyze-protein-groups.rb
 
 
analyze-psm.rb
analyze-psm.rb
 
 
annotate-csv.rb
annotate-csv.rb
 
 
augustus-collect.defunct.rb
augustus-collect.defunct.rb
 
 
check-fasta.rb
check-fasta.rb
 
 
check-spectra.rb
check-spectra.rb
 
 
checkmod.rb
checkmod.rb
 
 
chop-fasta.rb
chop-fasta.rb
 
 
compare-omssa-simquant.defunct.rb
compare-omssa-simquant.defunct.rb
 
 
compare-omssa.rb
compare-omssa.rb
 
 
compare-psm-mod.rb
compare-psm-mod.rb
 
 
compare-sequest-csv.rb
compare-sequest-csv.rb
 
 
compile-gpf-index.rb
compile-gpf-index.rb
 
 
convert-peaks-results-to-csv.rb
convert-peaks-results-to-csv.rb
 
 
create-archive.php
create-archive.php
 
 
create-fasta.rb
create-fasta.rb
 
 
crosslink-masscalc.rb
crosslink-masscalc.rb
 
 
csv-to-mzidentml.rb
csv-to-mzidentml.rb
 
 
decoyfasta.rb
decoyfasta.rb
 
 
decoyfasta_py.defunct.py
decoyfasta_py.defunct.py
 
 
difference.rb
difference.rb
 
 
digest-protein.rb
digest-protein.rb
 
 
draw-diagram.defunct.rb
draw-diagram.defunct.rb
 
 
duplicate-csv-column.rb
duplicate-csv-column.rb
 
 
exclusion.rb
exclusion.rb
 
 
export-psm-to-ams.rb
export-psm-to-ams.rb
 
 
extract-csv-column.rb
extract-csv-column.rb
 
 
extract-gpf-peptides.rb
extract-gpf-peptides.rb
 
 
extract-omssa-results.rb
extract-omssa-results.rb
 
 
extract-sequest-results.rb
extract-sequest-results.rb
 
 
fasta-to-blast.rb
fasta-to-blast.rb
 
 
filter-psm-apply-protein-groups.rb
filter-psm-apply-protein-groups.rb
 
 
filter-psm-by-fpr.rb
filter-psm-by-fpr.rb
 
 
filter-psm-by-mass-accuracy.rb
filter-psm-by-mass-accuracy.rb
 
 
filter-psm-by-threshold.rb
filter-psm-by-threshold.rb
 
 
filter-psm-crop-by-hit-distinctiveness.rb
filter-psm-crop-by-hit-distinctiveness.rb
 
 
filter-psm-group-proteins.rb
filter-psm-group-proteins.rb
 
 
filter-psm-sanitize.rb
filter-psm-sanitize.rb
 
 
filter-qe-add-protein-groups.rb
filter-qe-add-protein-groups.rb
 
 
filter-qe-add-proteins.rb
filter-qe-add-proteins.rb
 
 
filter-qe-by-band.rb
filter-qe-by-band.rb
 
 
filter-qe-combine-pbc.rb
filter-qe-combine-pbc.rb
 
 
filter-qe-compare-ratios.rb
filter-qe-compare-ratios.rb
 
 
filter-qe-normalize.rb
filter-qe-normalize.rb
 
 
filter-qe-require-both-states.rb
filter-qe-require-both-states.rb
 
 
filter-qe-require-ms2.rb
filter-qe-require-ms2.rb
 
 
gff-length-histogram.rb
gff-length-histogram.rb
 
 
highlight.rb
highlight.rb
 
 
indirect-quantitation.defunct.rb
indirect-quantitation.defunct.rb
 
 
intersection.rb
intersection.rb
 
 
isotope-envelope.rb
isotope-envelope.rb
 
 
join-csv.rb
join-csv.rb
 
 
localize-by-spectral-counts.rb
localize-by-spectral-counts.rb
 
 
masscalc.rb
masscalc.rb
 
 
match-peaks.rb
match-peaks.rb
 
 
match-peptides.rb
match-peptides.rb
 
 
md5sum.rb
md5sum.rb
 
 
merge-csv-files.rb
merge-csv-files.rb
 
 
merge-fasta.rb
merge-fasta.rb
 
 
merge-mgf-files.rb
merge-mgf-files.rb
 
 
merge-sequest-csv.rb
merge-sequest-csv.rb
 
 
mzml-to-mgf.rb
mzml-to-mgf.rb
 
 
patchy-peptides.rb
patchy-peptides.rb
 
 
peptide-mass.rb
peptide-mass.rb
 
 
prefix-fasta.py
prefix-fasta.py
 
 
protein-list-to-groups.rb
protein-list-to-groups.rb
 
 
psm-extract-identifications.rb
psm-extract-identifications.rb
 
 
psm-score-histogram.rb
psm-score-histogram.rb
 
 
qtrace-crop-xhtml-report.rb
qtrace-crop-xhtml-report.rb
 
 
qtrace-estimate-labeling-efficiency.defunct.rb
qtrace-estimate-labeling-efficiency.defunct.rb
 
 
qtrace.rb
qtrace.rb
 
 
raw-to-mzml.rb
raw-to-mzml.rb
 
 
run-blast.rb
run-blast.rb
 
 
run-gpf.rb
run-gpf.rb
 
 
run-omssa.rb
run-omssa.rb
 
 
run-peaks.rb
run-peaks.rb
 
 
sixframes.rb
sixframes.rb
 
 
split-csv-file.rb
split-csv-file.rb
 
 
strip-mzml.rb
strip-mzml.rb
 
 
subtract-psm-scans-from-xquest.rb
subtract-psm-scans-from-xquest.rb
 
 
swap-csv-columns.rb
swap-csv-columns.rb
 
 
transpose-dna.defunct.php
transpose-dna.defunct.php
 
 
transpose-dna.defunct.py
transpose-dna.defunct.py
 
 
transpose-dna.rb
transpose-dna.rb
 
 
union.rb
union.rb
 
 
unwrap-fasta.py
unwrap-fasta.py
 
 
write-blast-report.rb
write-blast-report.rb
 
 
write-omssa-report.rb
write-omssa-report.rb
 
 
xquest-xml-to-csv.rb
xquest-xml-to-csv.rb
 
 

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Synopsis

The Proteomatic scripts are the CLI backend to Proteomatic.

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The scripts backend to Proteomatic

www.proteomatic.org

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