Files in claraqin/neonMicrobe
Downloading, Pre-processing, and Assembling NEON Soil Microbe Marker Gene Sequence Data
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/batch_management.R
R/dada_wrappers.R
R/data.R
R/dirs.R
R/get_neon_data.R
R/plot.R
R/setup.R
R/utils.R
README.md
_config.yml
code/plotEEvsTruncLen.R
data-raw/seqmeta_greatplains_16s.R
data-raw/seqmeta_greatplains_16s.csv
data-raw/seqmeta_greatplains_its.R
data-raw/seqmeta_greatplains_its.csv
data-raw/seqtab_greatplains_16s.R
data-raw/sequence_greatplains_16s.R
data-raw/sequence_greatplains_its.R
data-raw/soil_greatplains.R
data-raw/soil_greatplains.csv
data/seqmeta_greatplains_16s.rda
data/seqmeta_greatplains_its.rda
data/seqtab_greatplains_16s.rda
data/soil_greatplains.rda
inst/CITATION
inst/extdata/16S/BMI_Plate37WellA12_16S_BJ8RK_R1.fastq.gz
inst/extdata/16S/BMI_Plate37WellA12_16S_BJ8RK_R2.fastq.gz
inst/extdata/ITS/BMI_Plate37WellB2_ITS_BNM6G_R1.fastq.gz
inst/extdata/ITS/BMI_Plate37WellB2_ITS_BNM6G_R2.fastq.gz
inst/extdata/seqmeta_greatplains.csv
inst/extdata/seqmeta_greatplains_16s.csv
inst/extdata/seqmeta_greatplains_its.csv
man/NEONMICROBE_DIR_BASE.Rd
man/NEONMICROBE_DIR_BATCHES.Rd
man/NEONMICROBE_DIR_MIDPROCESS.Rd
man/NEONMICROBE_DIR_OUTPUTS.Rd
man/NEONMICROBE_DIR_SEQMETA.Rd
man/NEONMICROBE_DIR_SEQUENCE.Rd
man/NEONMICROBE_DIR_SOIL.Rd
man/NEONMICROBE_DIR_TAXREF.Rd
man/NEONMICROBE_DIR_TRACKREADS.Rd
man/assign_final.Rd
man/checkArgsAgainstBatchParams.Rd
man/collapseNoMismatch2.Rd
man/combineReadTrackingTables16S.Rd
man/combineReadTrackingTablesITS.Rd
man/downloadRawSequenceData.Rd
man/downloadRawSoilData.Rd
man/downloadSequenceMetadata.Rd
man/downloadSoilData.Rd
man/getBatch.Rd
man/getBatchParam.Rd
man/getN.Rd
man/getPairedFastqFiles.Rd
man/getSampleName.Rd
man/getTruncationLength.Rd
man/listBatches.Rd
man/loadParams.Rd
man/makeDataDirectories.Rd
man/matchFastqToMetadata.Rd
man/newBatch.Rd
man/organizeRawSequenceData.Rd
man/parseParamsFromRownames.Rd
man/plotEEProfile.Rd
man/qcMetadata.Rd
man/qualityFilter16S.Rd
man/qualityFilterITS.Rd
man/readSequenceMetadata.Rd
man/removeUnpairedFastqFiles.Rd
man/remove_unmatched_files.Rd
man/runDada16S.Rd
man/runDadaITS.Rd
man/saveParams.Rd
man/seqmeta_greatplains_16s.Rd
man/seqmeta_greatplains_its.Rd
man/seqtab_greatplains_16s.Rd
man/setBaseDirectory.Rd
man/setBatch.Rd
man/setBatchParam.Rd
man/soil_greatplains.Rd
man/trimPrimers16S.Rd
man/trimPrimersITS.Rd
man/validateIO.Rd
neonMicrobe.Rproj
tests/testthat.R
tests/testthat/test-batch.R
tests/testthat/test-dada-wrappers.R
tests/testthat/test-setup.R
vignettes/add-environmental-variables-16s.Rmd
vignettes/add-environmental-variables-its.Rmd
vignettes/download-neon-data.Rmd
vignettes/process-16s-sequences.Rmd
vignettes/process-its-sequences.Rmd
vignettes/sensitivity-analysis.Rmd
