Recent Edited Articles

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2016 documentation improvement project

Drafts

-08/17/18: Using GeneticsLand
-10/03/16: Quantile-Quantile plot (QQplot)

-08/10/16: NGS Copy Number Analysis Using OmicSoft
-01/21/16: Template:Draft

-11/04/15: Genetics SubsetPlinkBed.pdf
-04/19/13: Test

Needs Updating

-11/01/18: Ngs SentieonDnaSeqPipeline.pdf
-08/13/18: ClinicalTableView
-07/30/18: TableView
-11/09/17: How to make survival plots variant omic data querys in Geneticsland
-10/27/17: Table Correlation.pdf
-10/18/17: ProjectTableView
-10/06/17: Sentieon QC Metrics
-09/25/17: Cnv ImportAffymetrixCychp.pdf
-09/25/17: OmicSoft Land Metadata Definitions
-09/24/17: Variant.CovariateVariableView
-08/07/17: Best Practices
-08/01/17: UpdateCloudLands

-07/28/17: Gene.GroupedVcfSnpSummary
-06/26/17: Region.AllSnpListing
-06/26/17: Region.CodingSnpListing
-06/26/17: Region.GeneListing
-06/26/17: Region.AssociationTable
-06/26/17: Variant.GenotypeFrequency
-06/26/17: Variant.SnpAnnotation
-06/26/17: Variant.SnpGenotypes
-06/26/17: Variant.VcfSnpGenotypes
-06/26/17: Variant.ArraySnpGenotypes
-06/26/17: Variant.ImputedSnpDoseGenotypes
-06/26/17: Variant.TimeSeriesView

-06/26/17: Variant.AssociationTable
-06/26/17: Variant.AlleleFrequency
-06/26/17: ClinicalTimeSeries
-05/25/17: Integration MicroArrayMicroArrayIntegration.pdf
-05/17/17: Trimming%
-05/15/17: Manage Sample Meta Data in Land
-05/04/17: Lists
-03/09/17: Observation Tab
-03/09/17: Variable Tab
-10/17/16: Cnv SegmentCnv.pdf

Pending approval 2017

-11/09/18: Ngs SCPreprocess.pdf
-10/19/18: LandTextDump
-09/25/18: CuratedGWAS
-09/21/18: Create Land
-09/04/18: Introduction to TCGA Land Content
-08/31/18: R Integration
-08/10/18: GxL.PheWAS Land
-08/09/18: RTsne.pdf
-07/19/18: Using Geneticsland R API
-07/17/18: A list of compiled genome and gene model from OmicSoft
-07/02/18: Land R API
-06/29/18: Building Land User Guide
-06/07/18: GeneSetAnalysis.pdf
-06/06/18: Open in Powerpoint Error Message
-06/05/18: Run KMeans RScript
-06/04/18: Variable Metadata
-06/01/18: Ngs ReportSingleCellCounts.pdf
-05/31/18: Ngs 10X V1 Preprocess.pdf
-05/16/18: Ngs SCRNASeqMetrics.pdf
-05/15/18: Error: The requested name is valid, but no data of the requested type was found
-04/11/18: SCDE.pdf
-04/11/18: Setup tSNE in R engine
-03/28/18: Land GxlGwasPCA.pdf
-03/26/18: AnnotateVariants.pdf
-03/21/18: ImportNanoStringRcc.pdf
-03/02/18: ImportZeroInflatedData.pdf
-02/27/18: VcfData
-02/20/18: LDAP configuration
-02/19/18: Manage Association MetaData
-02/08/18: Preprocess of SingleCell RNA-Seq Data
-02/02/18: RunParameterizedScript.pdf
-01/29/18: Setup SCDE in R engine
-01/12/18: IA FetchVariableData
-12/27/17: Sample MetaData File
-12/22/17: VariantClassifiers
-12/18/17: IA FetchSampleSetIDs
-12/15/17: IA UpdateSamples
-12/15/17: IA SearchSamples
-12/15/17: IA SearchSampleSets
-12/15/17: AddSampleSet

-12/14/17: IA AddSamples
-12/14/17: RemoveSampleSets
-12/14/17: External Script Integration
-12/07/17: Introduction to Hematology Land Content
-11/30/17: RnaSeq Transcript.GroupSummary
-11/20/17: AutoPublish
-11/17/17: SC RegularExpressionExamples.pdf
-11/09/17: ClinicalVariable
-11/09/17: ClinicalDistribution
-10/27/17: Gene.AllSnpListing
-10/23/17: ManageGeneticsLandProjectAccessControl.pdf
-10/23/17: Association.RegionPlot
-10/23/17: Variant Search Scope
-10/19/17: Restart ArrayServer in GUI
-10/16/17: ComparisonDistribution
-10/06/17: PathwayDistribution
-10/06/17: GeneDistribution
-10/06/17: SampleDistribution
-10/06/17: Add GeneticsLand Custom Query.pdf
-10/06/17: Sentieon QC Metrics
-10/02/17: Comparison.Table
-10/02/17: IpaUpload.pdf
-10/01/17: Genetics GwasQCPipeline.pdf
-09/24/17: Gene.VcfSnpSummary
-09/11/17: Manage Project MetaData
-08/25/17: NewProject
-08/15/17: ZeroInflated Pca.pdf
-08/15/17: SplitNgsFileByTag.pdf
-08/08/17: Association.PValueQQPlot
-07/17/17: SpawnOffCommand
-06/14/17: Ngs MapRnaSeqSingleCellReadsToGenome.pdf
-06/13/17: ManageUserGroups.UpdateMembers
-06/13/17: Genetics LoadPlinkPed.pdf
-06/13/17: Ngs SCFilterFastq.pdf
-06/12/17: ManageUsers.Remove
-06/12/17: ManageUsers.Update
-06/12/17: ManageUsers.Add
-06/09/17: IA FetchDataFromPublishedProject
-06/08/17: DownloadProject
-06/08/17: Table Reorder.pdf

-06/08/17: Ngs SC SummarizeTagQC.pdf
-06/08/17: Ngs MapRnaSeqSingleCellReadsToGenomeTags.pdf
-06/08/17: Genetics NormalizeSnpStrand.pdf
-06/06/17: IA SearchPublishedProjects
-06/02/17: RPKM Transcript
-05/31/17: SCRNA-Seq Analysis
-05/31/17: Ngs RemoveDuplicatesForSingleCell.pdf
-05/30/17: Subject
-05/26/17: User GenomeMark to bookmark regions in genome browser
-05/26/17: GenomeBrowerToolStrip.pdf
-05/25/17: Show MA Plot or XY Plot
-05/18/17: Add List Membership To Table
-05/17/17: Cynomolgus Monkey Genome Built
-05/16/17: Ngs NgsSequenceDuplication.pdf
-05/15/17: NgsSequenceDuplication
-05/09/17: UpdateUserProfile.pdf
-04/28/17: Share Genome Browser.txt
-04/06/17: ManageGeneSets ExportGeneSets
-03/31/17: NormalizeNgsData.pdf
-03/24/17: Genome Browser Use Case: Access genome browser session via hyperlinks in an excel file
-03/23/17: Cloud error message: Runtime was not set up for cloud file
-03/13/17: Solution Explorer
-03/10/17: View Source
-03/09/17: View Controller
-03/02/17: UNMAPPED BAM
-02/23/17: Change Fill Properties
-02/23/17: Change Symbol Properties
-02/23/17: Change Line Properties
-02/23/17: Flip X/Y Axis
-02/22/17: Refresh design table with server metadata
-02/22/17: Design
-02/10/17: Manage Land filters
-02/08/17: Change resolution of exported images
-01/30/17: ManageGeneSets ImportGeneSets
-01/25/17: Gene.CodingSnpListing
-01/24/17: ManageGeneticsLandUserControl.pdf
-01/06/17: ContextType
-01/05/17: Getting Started With Single Cell Lands
-01/05/17: Set Time Series Scope

Finalized in 2017

-11/09/18: Ngs SCPreprocess.pdf
-11/01/18: Build ComparisonLand From Raw Data
-10/18/18: Automatic index
-08/09/18: RTsne.pdf
-06/01/18: Ngs ReportSingleCellCounts.pdf
-05/31/18: Ngs 10X V1 Preprocess.pdf
-05/16/18: Ngs SCRNASeqMetrics.pdf
-04/11/18: SCDE.pdf
-04/11/18: Setup tSNE in R engine
-03/16/18: Contrast Type
-03/06/18: Install R Packages for ArrayServer
-02/08/18: Preprocess of SingleCell RNA-Seq Data
-01/31/18: ReportSingeCellGeneCounts
-01/29/18: Setup SCDE in R engine
-01/24/18: GxlGwasPCA
-12/19/17: DendrogramFormatting.pdf
-12/07/17: Probe mapping file

-12/07/17: Introduction to GENIE Land Content
-12/07/17: Introduction to Sanger Land Content
-12/07/17: CellLine GSK B37
-12/06/17: CellLine Pfizer B37
-12/06/17: CellLine NCI B37
-12/06/17: Expression Intensity Probes.Variable
-12/06/17: Pediatrics
-12/04/17: Introduction To MetastaticCancer B37
-11/30/17: MS.Variable
-11/30/17: CNStatus table correlation
-11/30/17: Export Consensus Sequence
-11/29/17: DynamicCorrelation.Comparison Comparison
-11/17/17: SC RegularExpressionExamples.pdf
-11/15/17: CorrelationEngine
-11/14/17: OncoLand Case Study - Cox Model
-11/14/17: PRAD iCluster
-11/09/17: How to make survival plots variant omic data querys in Geneticsland

-11/02/17: GeneSetAnalysis Oscript
-11/01/17: OncoLand Case Study - OncoGEO
-10/27/17: Gene.AllSnpListing
-10/23/17: ImportNanoStringRcc
-10/13/17: OncoLand Case Study - Differential Expression within and between Tumor Types
-09/08/17: Error Instance creation is not successful
-08/15/17: ZeroInflated Pca.pdf
-08/15/17: SplitNgsFileByTag
-06/13/17: Ngs SCFilterFastq.pdf
-06/08/17: Ngs SC SummarizeTagQC.pdf
-06/08/17: Ngs MapRnaSeqSingleCellReadsToGenomeTags.pdf
-05/31/17: Ngs RemoveDuplicatesForSingleCell.pdf
-05/05/17: RnaSeq Transcript.SurvivalView
-01/05/17: FilterTimeSeriesData.pdf
-01/05/17: ImportLongitudinalData.pdf

Pending approval 2016

-10/12/18: Land ExportFromGxl.pdf
-09/28/18: LandTools
-08/17/18: Using GeneticsLand
-07/02/18: Land R API
-06/18/18: GeneticsLand Overview
-03/22/18: Steps to build AWS ArrayServer with cloud plugin
-01/10/18: OneWayAnova.pdf
-11/30/17: DESeq2Test.pdf
-10/16/17: SearchGxl
-07/26/17: RnaSeq Transcript.Heatmap

-03/09/17: MicroArray VariableView
-03/07/17: DESeq2Test
-02/09/17: Customize Land View Visibility
-01/04/17: AnnotateVcfDataV2
-12/19/16: Array Viewer
-12/16/16: Alignment and read counts
-12/13/16: Preferences
-12/12/16: ExportItem
-12/12/16: Array Studio View Types
-11/07/16: EditCustomizedGridProperty

-10/31/16: TextDumpLandData AllGenes.pdf
-10/19/16: RNASeqQCMetricsTable
-10/18/16: Open ArrayStudioLauncher with a link to content
-10/17/16: Annotate Variants in Array Studio
-10/17/16: Search
-10/13/16: ExportFromGxl
-10/10/16: SandBox
-02/29/16: DNASeqQCMetricsTable

Finalized in 2016

-10/16/18: RemapSampleIDs
-09/21/18: Create Land
-08/31/18: ManageServerRScriptEngine.pdf
-08/16/18: Land PublishToGxl.pdf
-07/26/18: Sample Registration File
-07/24/18: UserAuthorization
-07/06/18: Land DeleteLand.pdf
-06/29/18: Getting Started
-06/28/18: ArrayServer.cfg
-06/07/18: GeneSetAnalysis.pdf
-06/06/18: SummaryStatistics.pdf
-05/29/18: ServerDataMatrix.Virus.Variable
-05/22/18: Master Server and Analytic Server
-05/08/18: Genetics PairwiseLD.pdf
-04/12/18: How to compile Alignment Report from bam.summary.txt file
-03/26/18: AnnotateVcfData
-03/26/18: AnnotateVariants.pdf
-03/23/18: Manage Land Sample Metadata
-03/21/18: PairedGroupTest.pdf
-03/20/18: PairwiseCorrelation.pdf
-03/20/18: SummarizeTargetCoverage.pdf
-03/07/18: ReportExonJunctions.pdf
-02/20/18: Voom.pdf
-01/17/18: Table ColumnProperties.pdf
-01/10/18: OneWayAnova.pdf
-12/27/17: Sample MetaData File
-12/27/17: Building Land From Raw Data
-12/27/17: Ngs RnaSeqPipeline.pdf
-12/21/17: LinearModel.pdf
-12/19/17: HierarchicalClustering.pdf
-12/13/17: How to use multiple sequence files for one sample?
-12/13/17: ArrayStudio ClickOnce Launch in Mac
-11/30/17: CorrelateCovariate.pdf
-10/16/17: Getting Started with RT-PCR Analysis
-10/16/17: Getting Started with Microarray Analysis
-10/12/17: Analytic Module Versions
-10/12/17: Activate Array Studio
-10/10/17: Ftp connection can not be established between server and client after trying 100 rounds of multi-threaded ftp
-10/01/17: Genetics GwasQCPipeline.pdf
-08/30/17: Inference Report
-08/25/17: RunOnServer
-08/22/17: Table PropagateColumns.pdf
-08/08/17: Import Expression Data
-07/20/17: Gene sets curated by OmicSoft from Land
-06/15/17: Create ComparisonLand from External Inference Reports
-06/13/17: Genetics LoadPlinkPed.pdf
-06/13/17: LoadPlinkPed
-06/08/17: Table Reorder.pdf
-06/08/17: Genetics NormalizeSnpStrand.pdf
-06/06/17: TwoWayAnova.pdf

-06/06/17: ExonLinearModel.pdf
-06/02/17: Manage Sample Clinical Data
-06/01/17: RNA-Seq Normalized FPKM Values in Land
-05/18/17: ArrayServer folder mapping and management
-05/17/17: Cynomolgus Monkey Genome Built
-05/16/17: Ngs NgsSequenceDuplication.pdf
-05/11/17: RemapAssociationIDs
-05/09/17: UpdateUserProfile.pdf
-05/05/17: DownloadGEOData.pdf
-05/04/17: Ngs ReportGeneTranscriptCounts.pdf
-03/27/17: PanelID
-03/27/17: Venn Diagram
-03/16/17: AddTrackFromENCODE.pdf
-03/10/17: Normalize.pdf
-03/08/17: Land SummarizeSampleMutationCount.pdf
-02/28/17: Table Unstack.pdf
-02/22/17: Plot Per-Gene Expression in a Sample to Compare GeneSets
-02/07/17: Ngs BuildGeneModel.pdf
-02/06/17: Table Summarize.pdf
-02/06/17: SurvivalTraitAssociation.pdf
-01/23/17: Ngs BuildReferenceLibrary.pdf
-01/23/17: Table Join.pdf
-01/04/17: AnnotateMutationV2
-01/03/17: Genetics GwasAssociationAnalysis.pdf
-01/03/17: BatmanTest.pdf
-12/13/16: Color by Selected
-12/12/16: Reorder variables or observations in Microarray data
-12/12/16: Mask heatmap rows or columns
-12/12/16: Land PublishAlv.pdf
-12/12/16: Table VariableSelection.pdf
-12/12/16: Table AddColumnsFromTable.pdf
-12/04/16: Genetics GwasImputePipeline.pdf
-11/29/16: Ngs AnnotateMutationV2.pdf
-11/23/16: How to remove land local cache
-11/22/16: Ngs BuildMutationAnnotator.pdf
-11/18/16: Ngs SummarizeMutation2Snp.pdf
-11/14/16: SelectData.pdf
-11/09/16: ReportPairedEndFusionGenes.pdf
-10/31/16: Ngs FilterNgsFiles.pdf
-10/27/16: Table Stack.pdf
-10/17/16: Ngs AnnotateVcfDataV2.pdf
-10/17/16: FilterNgsFiles
-10/17/16: Open selected sample in genome browser
-10/14/16: ManageGeneSets.pdf
-10/12/16: Land RemoveSamplesFromLand.pdf
-10/12/16: RnaSeqPipeline
-10/04/16: Comparison.VennDiagram
-09/20/16: SummarizeNgsCoverage.pdf
-09/13/16: BuildXenograftReferenceLibrary
-09/13/16: BuildXenograftGeneModel

-09/09/16: ComparisonLand Vector
-09/09/16: Comparison MetaData File
-09/09/16: Comparison Data File
-09/09/16: ArrayLand File Types
-09/09/16: ArrayLand Vector
-08/31/16: Sam.pdf
-08/25/16: Upload Files
-08/25/16: Manage Server Jobs
-08/19/16: SearchableList.pdf
-08/18/16: Table TranslateRowIDs.pdf
-08/17/16: ServerDataMatrix.16SMicrobial.Variable
-08/15/16: Getting Started with RNAseq Analysis
-08/15/16: Getting Started with the Genome Browser
-08/15/16: Getting Started with DNAseq Analysis
-08/15/16: Getting Started with Copy Number Variation Analysis
-08/10/16: Manage Folder Mapping
-08/09/16: Table Sort.pdf
-08/09/16: Land RemoveAssociationsFromLand.pdf
-08/09/16: OutlierDetection.pdf
-08/09/16: OneGroupTest.pdf
-08/09/16: Table Merge.pdf
-08/09/16: ManageUsers.pdf
-08/09/16: Expose Script in GUI
-08/09/16: ExonArray Pca.pdf
-08/09/16: ServerListAnalysis.pdf
-08/09/16: Table Pca.pdf
-08/09/16: Table SummarizeMissingPattern.pdf
-08/09/16: Table EstimateDensity.pdf
-08/05/16: ProportionLogisticRegressionModel.pdf
-08/04/16: ReportGeneTranscriptCounts
-08/02/16: OmicSoft BoxPlot
-08/02/16: Filter for significant genes from multiple tests
-08/02/16: Align Ion Torrent reads
-08/01/16: Sma.pdf
-08/01/16: TwoWayNestedAnova.pdf
-08/01/16: FindNeighbor.pdf
-07/26/16: Table DeleteColumns.pdf
-07/26/16: Table CombineColumns.pdf
-07/26/16: Table Cartesian.pdf
-07/26/16: Table ReorderColumns.pdf
-07/26/16: Table ReorderRows.pdf
-07/25/16: TwoGroupPermutationTest.pdf
-07/25/16: MicroArrayCategoricalTraitAssociation.pdf
-07/25/16: Table Split.pdf
-07/25/16: Table SelectList.pdf
-07/22/16: MultipleGroupTest.pdf
-07/21/16: RnaSeqQCMetrics.pdf
-07/20/16: Recover From Analysis With Error
-07/20/16: Table ParseColumn.pdf
-07/20/16: SummarizeInferenceReport.pdf


All Recent Articles

-11/14/18: Save and open land view
-11/13/18: TPM and FPKM
-11/09/18: Ngs SCPreprocess.pdf
-11/09/18: Land PublishCloudLand.pdf
-11/06/18: GeneSet.VcfSnp.CodingMatrix
-11/06/18: Gene.VcfSnp.CarrierSampleDetails
-11/06/18: Tutorials
-11/01/18: Build ComparisonLand From Raw Data
-11/01/18: Ngs SentieonDnaSeqPipeline.pdf
-10/19/18: LandTextDump
-10/18/18: Automatic index
-10/16/18: RemapSampleIDs
-10/16/18: Ngs SubsetNgsData.pdf
-10/12/18: Land ExportFromGxl.pdf
-10/01/18: ClinicalJoinSampling
-10/01/18: ArrayLand Configuration Options
-09/28/18: LandTools

-09/28/18: Introduction to SCUmiHuman Land Content
-09/27/18: Hardware/software requirements for LandExplorer
-09/26/18: Setup ArrayServer in Cluster
-09/25/18: RnaSeq Transcript.PooledControlSummary
-09/25/18: CuratedGWAS
-09/21/18: Create Land
-09/20/18: SampleRegistrationAccessLevel
-09/05/18: AdminSuperPassword
-09/04/18: Introduction to TCGA Land Content
-08/31/18: ManageServerRScriptEngine.pdf
-08/31/18: R Integration
-08/31/18: Manage local r script engine
-08/31/18: Install R locally.pdf
-08/31/18: SetLocalRScriptEngine.pdf
-08/30/18: Supported filter syntax in Array Studio
-08/29/18: ClusterMemFree
-08/24/18: The requested view cannot be retrieved from server

-08/24/18: Template:InstallLibgdiplus
-08/24/18: Libgdiplus complie error
-08/24/18: Charting error in Oshell or ArrayServer run
-08/24/18: TCGA Marker Papers
-08/20/18: UseDev
-08/17/18: Using GeneticsLand
-08/16/18: Land PublishToGxl.pdf
-08/15/18: Land Explorer did not find any lands from your server
-08/15/18: Cannot create channel sink to connect to URL
-08/15/18: HTTP Error 500.19 0x8007007e
-08/13/18: Ngs SC10xV2Preprocess.pdf
-08/13/18: ClinicalTableView
-08/10/18: GxL.PheWAS Land
-08/09/18: RTsne.pdf
-08/09/18: OmicSoft DEV Build
-08/03/18: Array Studio IT Requirements