Files in phraber/lassie
Tools to select sites and sequences that represent variation in a longitudinally sampled protein alignment

.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/CH505.R R/aa.colors.R R/add.clone.R R/annotate.region.R R/compute.hd.matrix.R R/compute.peak.tf.loss.R R/compute.tf.area.R R/compute.tf.loss.R R/compute.variant.frequencies.R R/compute.variant.frequency.R R/compute.whenup.R R/concatamerize.R R/create.refseq.lut.R R/create.refseq.lut.from.file.R R/create.tf.loss.matrix.R R/create.timepoint.parser.R R/create_sequence_subset.R R/dotify.matrix.R R/env.features.R R/excise.refseq.R R/exclude.vloop.sites.R R/export.fasta.swarmset.R R/export.swarmset.R R/get.refseq.row.R R/hamming.dist.R R/init.clone.list.R R/is.protein.R R/lassie.R R/longest.deletion.per.sequence.R R/longest.indel.in.sequence.R R/longest.insertion.in.sequence.R R/longest.insertion.per.sequence.R R/make.logoplot.R R/make.swarm.logos.R R/make.timepoint.logos.R R/parse.timepoints.R R/plot.peak.loss.cdf.R R/plot.swarmset.R R/plot.swarmtools.R R/plot.tf.loss.R R/plot.tf.loss.matrix.R R/plot.tf.loss.vector.R R/plot.variant.frequency.R R/pngs2o.R R/prep.aln.R R/print.swarmset.R R/print.swarmtools.R R/read.alignment.file.R R/report.variant.frequencies.R R/resample.swarmset.R R/rewrite.custom.colors.R R/select.clones.R R/select.sites.R R/set.alignment.R R/set.alignment.file.R R/set.excluded.sites.R R/set.included.sites.R R/set.refseq.R R/set.tf.R R/set.tf.loss.cutoff.R R/set.tp.parser.R R/summary.swarmset.R R/summary.swarmtools.R R/swarmset.R R/swarmtools.R
R/sysdata.rda
R/tabulate.swarmset.R R/tabulate.variants.R R/update.variant.counts.R R/vgrepl.R R/write.fasta.file.R R/write.lut.file.R R/zzz.R README.md data-raw/CH505.R data-raw/aa_colors.R
data-raw/color-lut.csv
data-raw/features.R data-raw/sysdata.R
data/CH505.rda
inst/CITATION
inst/doc/lassie.R inst/doc/lassie.Rmd
inst/doc/lassie.html
inst/doc/swarmset.png
inst/extdata/CH505-gp160.fasta
inst/extdata/CH505-swarmset.fasta
inst/extdata/color-lut.csv
inst/python/weblogo-3.4-modified/DEVELOPERS.txt
inst/python/weblogo-3.4-modified/LICENSE.txt
inst/python/weblogo-3.4-modified/MANIFEST.in
inst/python/weblogo-3.4-modified/README.txt
inst/python/weblogo-3.4-modified/build.sh
inst/python/weblogo-3.4-modified/build/lib/corebio/__init__.py
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inst/python/weblogo-3.4-modified/build/lib/corebio/data/blosum40.mat
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inst/python/weblogo-3.4-modified/build/lib/corebio/data/blosum50.mat
inst/python/weblogo-3.4-modified/build/lib/corebio/data/blosum62.mat
inst/python/weblogo-3.4-modified/build/lib/corebio/data/blosum80.mat
inst/python/weblogo-3.4-modified/build/lib/corebio/data/dbxref.txt
inst/python/weblogo-3.4-modified/build/lib/corebio/data/dist20_comp.mat
inst/python/weblogo-3.4-modified/build/lib/corebio/data/pam120.mat
inst/python/weblogo-3.4-modified/build/lib/corebio/data/pam250.mat
inst/python/weblogo-3.4-modified/build/lib/corebio/db/__init__.py
inst/python/weblogo-3.4-modified/build/lib/corebio/db/astral.py
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inst/python/weblogo-3.4-modified/build/lib/corebio/seq_io/_nexus/Nodes.py
inst/python/weblogo-3.4-modified/build/lib/corebio/seq_io/_nexus/Trees.py
inst/python/weblogo-3.4-modified/build/lib/corebio/seq_io/_nexus/__init__.py
inst/python/weblogo-3.4-modified/build/lib/corebio/seq_io/array_io.py
inst/python/weblogo-3.4-modified/build/lib/corebio/seq_io/clustal_io.py
inst/python/weblogo-3.4-modified/build/lib/corebio/seq_io/fasta_io.py
inst/python/weblogo-3.4-modified/build/lib/corebio/seq_io/genbank_io.py
inst/python/weblogo-3.4-modified/build/lib/corebio/seq_io/intelligenetics_io.py
inst/python/weblogo-3.4-modified/build/lib/corebio/seq_io/msf_io.py
inst/python/weblogo-3.4-modified/build/lib/corebio/seq_io/nbrf_io.py
inst/python/weblogo-3.4-modified/build/lib/corebio/seq_io/nexus_io.py
inst/python/weblogo-3.4-modified/build/lib/corebio/seq_io/null_io.py
inst/python/weblogo-3.4-modified/build/lib/corebio/seq_io/phylip_io.py
inst/python/weblogo-3.4-modified/build/lib/corebio/seq_io/plain_io.py
inst/python/weblogo-3.4-modified/build/lib/corebio/seq_io/stockholm_io.py
inst/python/weblogo-3.4-modified/build/lib/corebio/seq_io/table_io.py
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inst/python/weblogo-3.4-modified/test_corebio/test_scop.py
inst/python/weblogo-3.4-modified/test_corebio/test_secstruc.py
inst/python/weblogo-3.4-modified/test_corebio/test_seq.py
inst/python/weblogo-3.4-modified/test_corebio/test_seq_io.py
inst/python/weblogo-3.4-modified/test_corebio/test_ssearch_io.py
inst/python/weblogo-3.4-modified/test_corebio/test_stockholm_io.py
inst/python/weblogo-3.4-modified/test_corebio/test_stride.py
inst/python/weblogo-3.4-modified/test_corebio/test_table_io.py
inst/python/weblogo-3.4-modified/test_corebio/test_transform.py
inst/python/weblogo-3.4-modified/test_corebio/test_utils.py
inst/python/weblogo-3.4-modified/test_weblogo.py
inst/python/weblogo-3.4-modified/test_weblogo/data/Rv3829c.fasta
inst/python/weblogo-3.4-modified/test_weblogo/data/cap.fa
inst/python/weblogo-3.4-modified/test_weblogo/data/cox2.msf
inst/python/weblogo-3.4-modified/transformseq
inst/python/weblogo-3.4-modified/weblogo
inst/python/weblogo-3.4-modified/weblogolib/__init__.py
inst/python/weblogo-3.4-modified/weblogolib/_cgi.py
inst/python/weblogo-3.4-modified/weblogolib/_cli.py
inst/python/weblogo-3.4-modified/weblogolib/color.py
inst/python/weblogo-3.4-modified/weblogolib/colorscheme.py
inst/python/weblogo-3.4-modified/weblogolib/colorscheme.py-original
inst/python/weblogo-3.4-modified/weblogolib/logomath.py
inst/python/weblogo-3.4-modified/weblogolib/template.eps
lassie.Rproj
man/CH505.Rd man/aa.col.Rd man/create.timepoint.parser.Rd man/env.features.Rd man/export.fasta.swarmset.Rd man/export.swarmset.Rd man/is.protein.Rd man/lassie.Rd man/make.timepoint.logos.Rd man/plot.swarmset.Rd man/plot.swarmtools.Rd man/pngs2o.Rd man/prep.aln.Rd man/print.swarmset.Rd man/print.swarmtools.Rd man/read.alignment.file.Rd man/report.variant.frequencies.Rd man/resample.swarmset.Rd man/set.alignment.Rd man/set.alignment.file.Rd man/set.tf.Rd man/set.tf.loss.cutoff.Rd man/set.tp.parser.Rd man/summary.swarmset.Rd man/summary.swarmtools.Rd man/swarmset.Rd man/swarmtools.Rd man/tabulate.swarmset.Rd man/vgrepl.Rd tests/testthat.R tests/testthat/test_swarmset.R tests/testthat/test_swarmtools.R tutorial.pdf vignettes/lassie.Rmd
phraber/lassie documentation built on Sept. 25, 2018, 8:31 a.m.