Files in fmicompbio/mutscan
Preprocessing and Analysis of Deep Mutational Scanning Data
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/RcppExports.R
R/calculateFitnessScore.R
R/calculateRelativeFC.R
R/collapseMutantsByAA.R
R/digestFastqs.R
R/generateQCReport.R
R/linkMultipleVariants.R
R/mutscan-package.R
R/plotDistributions.R
R/plotFiltering.R
R/plotPairs.R
R/plotResults.R
R/plotTotals.R
R/relabelMutPositions.R
R/summarizeExperiment.R
R/utils.R
R/zzz.R
README.md
inst/CITATION
inst/extdata/GSE102901_cis_se.rds
inst/extdata/cisInput_1.fastq.gz
inst/extdata/cisInput_2.fastq.gz
inst/extdata/cisOutput_1.fastq.gz
inst/extdata/cisOutput_2.fastq.gz
inst/extdata/leujunt0_1.fastq.gz
inst/extdata/leujunt0_2.fastq.gz
inst/extdata/multipleVariableRegions_R1.fastq.gz
inst/extdata/multipleVariableRegions_R2.fastq.gz
inst/extdata/multipleVariableRegions_truth.rds
inst/extdata/transInput_1.fastq.gz
inst/extdata/transInput_2.fastq.gz
inst/extdata/transOutput_1.fastq.gz
inst/extdata/transOutput_2.fastq.gz
inst/scripts/generateExampleData.R
inst/scripts/generateExampleDataForLinkMultipleVariants.R
inst/scripts/generateValuesForUnitTestsCis.R
inst/scripts/generateValuesForUnitTestsLeuJun.R
inst/scripts/generateValuesForUnitTestsTrans.R
inst/templates/qc_report_template.Rmd
man/calcNearestStringDist.Rd
man/calculateFitnessScore.Rd
man/calculateRelativeFC.Rd
man/collapseMutantsBySimilarity.Rd
man/digestFastqs.Rd
man/figures/mutscan.png
man/generateQCReport.Rd
man/groupSimilarSequences.Rd
man/linkMultipleVariants.Rd
man/plotDistributions.Rd
man/plotFiltering.Rd
man/plotMeanDiff.Rd
man/plotPairs.Rd
man/plotTotals.Rd
man/plotVolcano.Rd
man/relabelMutPositions.Rd
man/summarizeExperiment.Rd
src/BKtree_utils.h
src/FastqBuffer_utils.h
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/calcNearestStringDist.cpp
src/digestFastqs.cpp
src/mergeEntriesForSummarization.cpp
src/stringdist.cpp
src/stringdist.h
tests/testthat.R
tests/testthat/test-relabelMutPositions.R
tests/testthat/test-translate.R
tests/testthat/test_BKtree_utils.R
tests/testthat/test_calcNearestStringDist.R
tests/testthat/test_calculateFitnessScore.R
tests/testthat/test_calculateRelativeFC.R
tests/testthat/test_collapseMutantsByAA.R
tests/testthat/test_digestFastqs_cis.R
tests/testthat/test_digestFastqs_helpers.R
tests/testthat/test_digestFastqs_input.R
tests/testthat/test_digestFastqs_parallelization.R
tests/testthat/test_digestFastqs_primers.R
tests/testthat/test_digestFastqs_trans.R
tests/testthat/test_digestFastqs_trans_collapse.R
tests/testthat/test_generateQCReport.R
tests/testthat/test_linkMultipleVariants.R
tests/testthat/test_plotDistributions.R
tests/testthat/test_plotFiltering.R
tests/testthat/test_plotPairs.R
tests/testthat/test_plotResults.R
tests/testthat/test_plotTotals.R
tests/testthat/test_summarizeExperiment.R
tests/testthat/tests-utils.R
vignettes/mutscan-overview.001.png
vignettes/mutscan.Rmd
