first commit

.gitignore

@@ -0,0 +1,20 @@
+rsconnect.R
+.bash_history
+# Playground for testing
+archive
+# RStudio config in Docker
+.cache
+.config
+.local
+.rstudio
+# RStudio project config
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+.config
+argos-shiny-app.zip
+# Dataset
+argos/dataset/*
+argos/www/*
+credentials.R

docker-compose.yml

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+version: "3.9"
+services: 
+  theia-server:
+    build: .
+    network_mode: host
+    ports: 
+      - "3838:3838"
+    environment: 
+      - PASSWORD=chad
+    volumes: 
+      - .:/home/rstudio

dockerfile

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+FROM rocker/verse:latest
+
+Run R -e "install.packages('shiny')"
+Run R -e "install.packages('shinydashboard')"
+Run R -e "install.packages('rsconnect')"
+Run R -e "install.packages('profvis')"
+Run R -e "install.packages('R.utils')"
+Run R -e "install.packages('shinyFiles')"
+Run R -e "install.packages('shinyjs')"
+Run R -e "install.packages('shinymanager')"
+Run R -e "install.packages('reactlog')"
+Run R -e "install.packages('styler')"
+Run R -e "install.packages('reactR')"
+Run R -e "install.packages('listviewer')"
+Run R -e "install.packages('rjson')"
+Run R -e "install.packages('shinythemes')"
+
+COPY rsconnect.R /home/rstudio/rsconnect.R
+Run R -e "source('/home/rstudio/rsconnect.R')"

filds.txt

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+"Sample Name",
+"Lane",
+"BarcodeIdx",
+"Project",
+"Harvest By",
+"Harvest Date",
+"Harvest Time",
+"First Strand Amp By",
+"First Strand Amp Date",
+"Amplified By",
+"Amplified Date",
+"Library By",
+"Library Date",
+"Species",
+"Strain",
+"Strain Other",
+"Age Harvested Unit",
+"Age Harvested Unit Other",
+"Age Harvested Value",
+"Age Culture",
+"Harvest Method",
+"Harvest Quant",
+"Harvest Compound",
+"Is Harvest Compound Uncaged",
+"Region",
+"Subregion",
+"Subregion Other",
+"Cell Class",
+"Cell Class Other",
+"Cell Type",
+"Cell Type Other",
+"Supplier",
+"Source Type",
+"Source Unit",
+"Source Unit Other",
+"Source Region",
+"Source Region Other",
+"Patient ID",
+"Cell ID",
+"Dendrite ID",
+"Source Well ID",
+"Treatment",
+"Replicate",
+"Source Amplification Method",
+"Source Amplification Rounds",
+"First Sequencing Barcode",
+"Second Sequencing Barcode",
+"Non-Sequencing Barcode",
+"Spike-In Type",
+"Spike-In Dilution",
+"Library Input Amount",
+"Library Kit",
+"Strand Specific",
+"Library Const PCR Cycles",
+"Amplification Protocol",
+"Library Protocol",
+"Analysis Protocol",
+"Contaminants File",
+"dbGaP Release",
+"SRA ID",
+"Notes",
+"pipeline",
+"STAR.star.version",
+"STAR.samtools.version",
+"STAR.species (genome)",
+"STAR.SE",
+"STAR.readLength",
+"STAR.Tot Reads After Trim",
+"STAR.Avg Inp Read Len",
+"STAR.Avg Uniq Map Len",
+"STAR.Perc Bases Mismatched",
+"STAR.Uniq-mapped Reads",
+"STAR.Total-mapped Reads",
+"STAR.Uniq-mapped Perc",
+"STAR.Multi-mapped Perc",
+"STAR.Not-mapped Perc",
+"VERSE.verse.version",
+"VERSE.transcriptome",
+"VERSE.stranded",
+"VERSE.ID_attribute",
+"VERSE.introns",
+"VERSE.intergenic",
+"VERSE.lines-sines",
+"VERSE.exons Level 1,2: non-SpikeIn Reads Counted",
+"VERSE.exons Level 1,2: SpikeIn ReadsCounted",
+"VERSE.exons Level 1,2: Num Genes",
+"VERSE.exons Level 1,2: Avg Read Per Gene",
+"VERSE.exons Level 1,2: Max Reads Per Gene",
+"VERSE.exons Level 1,2: Ambiguous Mapped",
+"VERSE.exons Level 3: Reads Counted",
+"VERSE.exons Level 3: Num Genes",
+"VERSE.exons Level 3: Avg Read Per Gene",
+"VERSE.exons Level 3: Max Reads Per Gene",
+"VERSE.exons Level 3: Ambiguous Mapped",
+"VERSE.anti-exons: non-spikeIn Reads Counted",
+"VERSE.anti-exons: spikeIn Reads Counted",
+"VERSE.anti-exons: Reads Counted",
+"VERSE.anti-exons: Num Genes",
+"VERSE.anti-exons: Avg Read Per Gene",
+"VERSE.anti-exons: Max Reads Per Gene",
+"VERSE.anti-exons: Ambiguous Mapped",
+"VERSE.introns Level 1,2: Reads Counted",
+"VERSE.introns Level 1,2: Num Genes",
+"VERSE.introns Level 1,2: Avg Read Per Gene",
+"VERSE.introns Level 1,2: Max Reads Per Gene",
+"VERSE.introns Level 1,2: Ambiguous Mapped",
+"VERSE.introns Level 3: Reads Counted",
+"VERSE.introns Level 3: Num Genes",
+"VERSE.introns Level 3: Avg Read Per Gene",
+"VERSE.introns Level 3: Max Reads Per Gene",
+"VERSE.introns Level 3: Ambiguous Mapped",
+"VERSE.anti-introns: Reads Counted",
+"VERSE.anti-introns: Num Genes",
+"VERSE.anti-introns: Avg Read Per Gene",
+"VERSE.anti-introns: Max Reads Per Gene",
+"VERSE.anti-introns: Ambiguous Mapped",
+"VERSE.mito: Reads Counted",
+"VERSE.mito: Num Genes",
+"VERSE.mito: Avg Read Per Gene",
+"VERSE.mito: Max Reads Per Gene",
+"VERSE.mito: Ambiguous Mapped",
+"VERSE.anti-mito: Reads Counted",
+"VERSE.anti-mito: Num Genes",
+"VERSE.anti-mito: Avg Read Per Gene",
+"VERSE.anti-mito: Max Reads Per Gene",
+"VERSE.anti-mito: Ambiguous Mapped",
+"VERSE.Intergenic: Reads Counted",
+"VERSE.Intergenic: Num Regions",
+"VERSE.Intergenic: Avg Read Per Region",
+"VERSE.Intergenic: Max Reads Per Region",
+"VERSE.Intergenic: Ambiguous Mapped",
+"VERSE.LINE Reads",
+"VERSE.SINE Reads",
+"VERSE.Num LINEs",
+"VERSE.Num SINEs",
+"VERSE.Neither LINEs nor SINEs",
+"VERSE.No Feature",
+"VERSE.Reads Missing Mates",
+"VERSE.Perc: Exons Level 1,2",
+"VERSE.Perc: Exons Level 3",
+"VERSE.Perc: Anti-Exons",
+"VERSE.Perc: Introns Level 1,2",
+"VERSE.Perc: Introns Level 3",
+"VERSE.Perc: Anti-Introns",
+"VERSE.Perc: Mito",
+"VERSE.Perc: Anti-Mito",
+"VERSE.Perc: Intergenic",
+"VERSE.Perc: Spike-In",
+"BLAST.blastn.version",
+"BLAST.parseBlast.py.version",
+"BLAST.species",
+"BLAST.readLength",
+"BLAST.numReads",
+"BLAST.kmer",
+"BLAST.Total Hits",
+"BLAST.Hits Not Counted",
+"BLAST.Perc Hits Not Target or SpikeIn",
+"BLAST.Bacteria",
+"BLAST.Danio",
+"BLAST.Fly",
+"BLAST.Human",
+"BLAST.Mouse",
+"BLAST.Rat",
+"BLAST.Yeast",
+"BLAST.Carp",
+"BLAST.ERCC",
+"BLAST.PhiX",
+"BLAST.TATAGTGAGT",
+"BLAST.Perc Counted",
+"TRIM.trimReads.py.version",
+"TRIM.minLen",
+"TRIM.phredThresh",
+"TRIM.removeN",
+"TRIM.numAT",
+"TRIM.SE",
+"TRIM.ContamFile",
+"TRIM.nTotalReadsBeforeTrim",
+"TRIM.nBothTrimmed",
+"TRIM.nFirstTrimmed",
+"TRIM.nSecondTrimmed",
+"TRIM.nBothDiscarded",
+"TRIM.nFirstDiscarded",
+"TRIM.nSecondDiscarded",
+"TRIM.Phred Threshold (first)",
+"TRIM.Phred Threshold (second)",
+"TRIM.removed5N (first)",
+"TRIM.removed5N (second)",
+"TRIM.removed3N (first)",
+"TRIM.removed3N (second)",
+"TRIM.init3G (first)",
+"TRIM.init3G (second)",
+"TRIM.indexAdapter (first)",
+"TRIM.indexAdapter (second)",
+"TRIM.univAdapterRC (first)",
+"TRIM.univAdapterRC (second)",
+"TRIM.aRNAPrimer (first)",
+"TRIM.aRNAPrimer (second)",
+"TRIM.aRNAPrimerRC (first)",
+"TRIM.aRNAPrimerRC (second)",
+"TRIM.tivaXoligo (first)",
+"TRIM.tivaXoligo (second)",
+"TRIM.tivaXoligoRC (first)",
+"TRIM.tivaXoligoRC (second)",
+"TRIM.dT5oligo (first)",
+"TRIM.dT5oligo (second)",
+"TRIM.dT5oligoRC (first)",
+"TRIM.dT5oligoRC (second)",
+"TRIM.dT6oligo (first)",
+"TRIM.dT6oligo (second)",
+"TRIM.dT6oligoRC (first)",
+"TRIM.dT6oligoRC (second)",
+"TRIM.NexteraRead1ExternalAdapter (first)",
+"TRIM.NexteraRead1ExternalAdapter (second)",
+"TRIM.NexteraRead2ExternalAdapter (first)",
+"TRIM.NexteraRead2ExternalAdapter (second)",
+"TRIM.ChexPolyCprimerRC (first)",
+"TRIM.ChexPolyCprimerRC (second)",
+"TRIM.istT7primerRC (first)",
+"TRIM.istT7primerRC (second)",
+"TRIM.NexteraTransposaseAdapterR1 (first)",
+"TRIM.NexteraTransposaseAdapterR1 (second)",
+"TRIM.NexteraTransposaseAdapterR1RC (first)",
+"TRIM.NexteraTransposaseAdapterR1RC (second)",
+"TRIM.NexteraTransposaseAdapterR2 (first)",
+"TRIM.NexteraTransposaseAdapterR2 (second)",
+"TRIM.NexteraTransposaseAdapterR2RC (first)",
+"TRIM.NexteraTransposaseAdapterR2RC (second)",
+"TRIM.NexteraTransposonEndSequence (first)",
+"TRIM.NexteraTransposonEndSequence (second)",
+"TRIM.NexteraTransposonEndSequenceRC (first)",
+"TRIM.NexteraTransposonEndSequenceRC (second)",
+"TRIM.SmartSeqTSO (first)",
+"TRIM.SmartSeqTSO (second)",
+"TRIM.SmartSeqTSORC (first)",
+"TRIM.SmartSeqTSORC (second)",
+"TRIM.SmartSeqOligo (first)",
+"TRIM.SmartSeqOligo (second)",
+"TRIM.SmartSeqOligoRC (first)",
+"TRIM.SmartSeqOligoRC (second)",
+"TRIM.5 polyT (first)",
+"TRIM.5 polyT (second)",
+"TRIM.3 polyA (first)",
+"TRIM.3 polyA (second)",
+"TRIM.removed5A (first)",
+"TRIM.removed5A (second)",
+"TRIM.removed3A (first)",
+"TRIM.removed3A (second)",
+"TRIM.removed5T (first)",
+"TRIM.removed5T (second)",
+"TRIM.removed3T (first)",
+"TRIM.removed3T (second)",
+"TRIM.removed5C (first)",
+"TRIM.removed5C (second)",
+"TRIM.removed3C (first)",
+"TRIM.removed3C (second)",
+"TRIM.removed5G (first)",
+"TRIM.removed5G (second)",
+"TRIM.removed3G (first)",
+"TRIM.removed3G (second)",
+"RMDUP.removeDuplicates.py.version",
+"RMDUP.nInitialReadPairs",
+"RMDUP.nUniqueReadPairs",
+"RMDUP.nDuplicatesFound",
+"RMDUP.nReadsWithDuplicates",
+"RMDUP.maxDuplicateCount",
+"GMAP.gmap.version",
+"GMAP.samtools.version",
+"GMAP.species (genome)",
+"GMAP.SE",
+"GMAP.readLength",
+"GMAP.Reads After Trim",
+"GMAP.Reads Mapped",
+"GMAP.Uniq Reads",
+"GMAP.Mismatches",
+"GMAP.Bases Mapped",
+"GMAP.Avg Read Length",
+"GMAP.Max Read Length",
+"BARCODE.kmerFind.py.version",
+"BARCODE.barcode",
+"BARCODE.prefix",
+"BARCODE.suffix",
+"BARCODE.cut",
+"BARCODE.SE",
+"BARCODE.R1_threshold",
+"BARCODE.R2_threshold",
+"BARCODE.nTotalReadsBeforeMapping",
+"BARCODE.totalBothMapped",
+"BARCODE.totalFirstMapped",
+"BARCODE.totalSecondMapped",
+"BARCODE.firstKmer",
+"BARCODE.firstRC",
+"BARCODE.secondKmer",
+"BARCODE.secondRC",
+"BARCODE.avgPosFirst",
+"BARCODE.avgPosSecond",
+"BARCODE.avgPosFirstForward",
+"BARCODE.avgPosFirstReverse",
+"BARCODE.avgPosSecondForward",
+"BARCODE.avgPosSecondReverse",
+"Experiment Name",
+"Description",
+"Investigators",
+"External Lab",
+"Submitted Date",
+"Machine Manufacturer",
+"Model",
+"Sequencing Kit",
+"Read Length",
+"Paired",
+"Facility",
+"Facility ID",
+"Processing",
+"Notes",