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_pkgdown.yml
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url: https://brentlab.github.io/brentlabRnaSeqTools/
template:
bootstrap: 5
theme: github-dark
articles:
- title: Tutorials
navbar: ~
contents:
- brentlabRnaSeqTools
- ProcessRun
- envPerturbation
- ninetyMinuteInduction_analysis
- QC_Library_Quality
- QC_Sample_Agreement_Objects
- Tally
- Rank_Response_Plot
- image_table_interactions
- exploring_dna_variants
- create_R_package
- access_data_in_archive
- posit_projects
reference:
- title: Data objects
desc: data objects loaded with brentlabRnaSeqTools
contents:
- database_info
- grant_df
- passing_genes_all
- database_colnames
- title: Database -- Utilities
desc: Things like connecting directly to the database, archiving or retrieving a user token
contents:
- connectToDatabase
- archiveDatabase
- getUserAuthToken
- title: Database -- Getting Data
desc: get the full join (getMetadata) or individual tables
contents:
- getMetadata
- getRawCounts
- getGeneNames
- listTables
- getTable
- getCapsuleImageSet
- title: Database -- Sending Data
desc: send data TO the database. Please be careful with these.
contents:
- postFastqSheet
- postCounts
- postQcSheet
- patchTable
- postTable
- postCapsuleJpeg
- postCapsuleJpeg_batch
- postCountsToDatabase
- postImageAnnotationsToDatabase
- title: brentLabRnaSeq Object
desc: the object(s) used in most of QC processing
contents:
- starts_with("brentlabRnaSeq")
- coerceToDds
- createExperimentSet
- test_train_partition
- estimateSizeFactorsByProtocol
- extractColData
- extractDesignMatrix
- getRunNumberLeadingZero
- qaFilter
- title: RNAseq Pipeline
desc: Functions for processing data from the database for the RNAseq pipeline
contents:
- readHTSeqFile
- parseNovoalignLog
- geneGRanges
- strandedScanBamParam
- htseq_proteinCodingTotal
- htseq_notAlignedTotalPercent
- htseq_libraryComplexity
- locusCoverage
- htseq_locusLog2cpm
- novoalignPipelineQC
- addQcColsToMeta
- autoAuditQcTable
- decomposeStatus2Bit
- kn99_novo_htseq_status
- kn99_novo_htseq_thresholds
- title: RNAseq Pipeline -- nextflow
desc: Functions for processing data in the nextflow pipeline
contents:
- createNovoalignPipelineSamplesheet
- createNfCorePipelineSampleSheet
- moveNfCoFastqFiles
- title: RNAseq QC -- Misc
desc: Miscellaneous RNAseq QC functions
contents:
- setPerturbedLociToZero
- removeParameterEffects
- fltrLowReplicateParams
- title: RNAseq QC -- RLE
desc: Functions used to calculate relative log expression for QC
contents:
- rleTransform
- calculateRLE
- calculateGeneWiseMedians
- rleSummary
- addRleSummaryStats
- rleByReplicateGroup
- rlePlotCompareEffectRemoved
- removeLibdateByReplicate
- plotRLEhistograms
- rlePlot
- rlePlot_helper
- title: RNAseq QC -- IGV
desc: Functions for interacting with the IGV
contents:
- createIgvBatchscript
- title: Experimental Sets
desc: Functions for creating various pre-defined experimental sets
contents:
- starts_with("createEnvPert")
- createEPTally
- starts_with("createNinetyMinuteInduction")
- createInductionSetTally
- starts_with("replicateByProtocolTally")
- filterWtByExperimentalLibdate_90min
- splitProtocolGroups
- title: Binding Response EDA functions
desc: For instance, for Rank-Response plots
contents:
- rank_response_plot
- create_partitions
- sort_rank_mean_expr
- title: Utilities
desc: Helper functions
contents:
- isNumeric
- is_integer64
- localView
- parseComparatives
- readInData
- run_numbers_with_leading_zero
- testBamPath