Popular KnowledgeBase Articles

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--- Aligned Data QC for RNA-Seq...(31831)
--- MiRNA alignment and quantification...(25712)
--- Raw Data QC of RNA-Seq Data...(20915)
--- Genome browser alignment filters...(19033)
--- Fusion strand and strands of fusion partners...(18881)
--- Build AWS Ubuntu AMI for OmicSoft Cloud Computing...(15530)
--- Master Server and Analytic Server...(15438)
--- Align Ion Torrent reads...(13512)
--- TPM and FPKM...(13384)
--- How to use multiple sequence files for one sample?...(12805)
--- Alignment and read counts...(10474)
--- Setup ArrayServer in Cluster...(9834)
--- Example of running 100 CCLE samples on cloud...(9695)
--- Amazon function list required to run Omicsoft On Cloud...(9631)
--- ArrayStudio ClickOnce Launch in Mac...(9365)
--- Visualization of RNA-Seq Aligned Data...(9140)
--- AddColumns.pdf...(8878)
--- Common ArrayStudio Launching Issues...(8531)
--- Array Viewer Links...(8421)
--- OncoLand Case Study - Summarize Mutation Count...(8385)
--- Plot Per-Gene Expression in a Sample to Compare GeneSets...(8307)
--- Build AWS RedHat AMI for OmicSoft Cloud Computing...(7887)
--- Omicsoft Gene Model...(7860)
--- Alternative splicing detection...(7727)
--- Typical way to update/restart ArrayServer...(7691)
--- OmicSoft Aligner Version 4 (OSA4) Benchmark...(7195)
--- Master and Analytic Servers...(7152)
--- How to resolve HRESULT 0x8007000B Error...(7116)
--- OncoLand Case Study - Custom Query...(6825)
--- What is Fold Change...(6715)
--- Annotate Variants in Array Studio...(6257)
--- Steps to build AWS ArrayServer with cloud plugin...(6093)
--- OncoLand Case Study - Co-mutated Genes...(6087)
--- Import Expression Data...(6002)
--- Recover From Analysis With Error...(5993)
--- Find a list of genes showing differential expression between two groups of samples...(5849)
--- Omicsoft RPKM/FPKM/Count values...(5709)
--- Get out of memory error...(5638)
--- ArrayServer Configuration with Cloud...(5302)
--- Generate copy number baseline for NGS data...(5301)
--- Hardware / Software requirements for Array Server...(5271)
--- Setting up ulimit for ArrayServer...(5174)
--- Agilent CGH QC Metric...(4951)
--- Logic to determine paired-end read files and sample name...(4513)
--- Reorder variables or observations in Microarray data...(4436)
--- Ftp connection can not be established between server and client after trying 100 rounds of multi-threaded ftp...(4340)
--- OncoLand Case Studies...(4232)
--- Track Properties...(4165)
--- Genome Browser Sequence Legend...(4121)
--- Heatmap normalization...(3927)
--- Gene sets curated by OmicSoft from Land...(3802)
--- CloudInstanceTag...(3592)
--- OncoLand Case Study - SampleSets with Grouping...(3455)
--- Mask heatmap rows or columns...(3416)
--- How to compile Alignment Report from bam.summary.txt file...(3393)
--- Error Instance creation is not successful...(3354)
--- Factors that affect alignment time...(3220)
--- Getting started with Array Studio...(3196)
--- Charting error in Oshell or ArrayServer run...(3162)
--- Create a searchable shortcut to OmicSoft wiki...(3130)
--- User GenomeMark to bookmark regions in genome browser...(3100)
--- MultiplicityAdjustment...(3031)
--- Filter for significant genes from multiple tests...(2959)
--- OncoLand Case Study - Clinical Variables...(2936)
--- Omicsoft GenCode Gene Model...(2913)
--- Isoform expression profile view in genome browser...(2881)
--- OmicSoft BoxPlot...(2832)
--- Installation Requirements For Array Studio...(2787)
--- How to make survival plots for sample categories defined by expression and/or mutations in OncoLand...(2742)
--- Convert inference report to MicroArray data...(2699)
--- GeneBas.GenomeBrowser...(2681)
--- Error Can not connect to Omicsoft server for license checking and online streaming...(2606)
--- Different quality encoding...(2592)
--- NGS Copy Number Analysis Using OmicSoft...(2506)
--- How to highlight selected genes in a scatter plot in Array Studio...(2383)
--- Is Estimate the same as a fold change? If not, what is a Fold Change?...(2367)
--- Manage Cloud Instances...(2366)
--- Error for hash HashValidation...(2351)
--- Open ArrayStudioLauncher with a link to content...(2305)
--- How to export annotated mutation report in batch mode?...(2290)
--- Ngs SentieonTNSeqPipeline.pdf...(2246)
--- How can we avoid auto-updates that occur upon starting up ArrayStudio...(2229)
--- Check List for ArrayServer Migration...(2110)
--- How to make survival plots for customized sample categories...(2096)
--- GCF...(2084)
--- Quantification in Strand Specific RNA-Seq dataset...(2055)
--- Example .proxy file...(2014)
--- CNV data preprocessing for Affymetrix SNP Array...(1969)
--- Does Array Studio have a workflow for paired-end strand-specific RNA-seq?...(1929)
--- ODP setup for Windows ArrayServer using Oracle Database...(1917)
--- Difference between Summarize Mutation Data and Summarize VCF Data (SAMTools)...(1916)
--- View Multiple Gene Regions...(1896)
--- DESeq vs DESeq R Package...(1877)
--- Which columns will be indexed as masterid for search in ArrayServer...(1809)
--- ArrayServer cannot get real time job log when running on the cluster...(1780)
--- Maximum number of novel exon junctions...(1768)
--- Trim UTRs by data in RNA-Seq Analysis...(1673)
--- Setting Proxy For Omicsoft ArrayServer...(1672)

--- Refresh Land...(1657)
--- Compute copy number log2ratio values from Affymetrix SNP arrays...(1631)
--- What is the difference between Mutations and Somatic mutations Analysis?...(1605)
--- Order of samples and variables in hierarchical clustering...(1592)
--- Error=Too many open files...(1579)
--- How to install .NET 3.5 on Windows Server...(1568)
--- Example of seeting cluster parallel environment...(1495)
--- Common ArrayServer Issues...(1484)
--- What is the benefit of using the Sample Management System in Array Studio?...(1465)
--- Refresh design table with server metadata...(1453)
--- InstanceProfileRole...(1451)
--- How is the quality score used in alignment?...(1437)
--- Autofill web service...(1428)
--- Errors related to bugs in Microsoft .Net framework 2.0...(1404)
--- BAM...(1389)
--- InstanceProfileArn...(1389)
--- Restore Fastq Files From BAM...(1388)
--- How do I find out what parameters were used for a particular workflow or used to generate a dataset or table?...(1355)
--- InstanceType...(1339)
--- Search Read Name in Genome Browser...(1328)
--- Why count data are not integers from OmicSoft quantification...(1311)
--- Multiple panels/views in Genome Browser...(1274)
--- Modify ArrayStudio ClickOnce Launch Link in Mac...(1266)
--- I am getting the error "Application cannot be started" when I try to launch the webstart application...(1260)
--- User Group Meeting 2017...(1260)
--- Merge fusion report of individual runs or samples...(1233)
--- How can I analyze NGS data on a list of customized region only...(1218)
--- Difference between "Map Reads to Genome (Illumina)" and "Map read to Genome (long reads)"...(1205)
--- Publish local project with NGS data...(1198)
--- CloudMaxInstanceCount...(1185)
--- Naive Count For miRNA...(1171)
--- OncoLand Case Study - Cox Model...(1122)
--- When shall RNA-Seq quantification results be transformed/normalized?...(1120)
--- Grey zone in dendrogram (heatmap) after filtering...(1107)
--- Error during fastq-dump step in downloadSRA job...(1106)
--- Omicsoft GenCode Gene ModelV27...(1104)
--- Check multi-read mapping...(1092)
--- OncoLand Case Study - Differential Expression within and between Tumor Types...(1092)
--- User Guides for Array Studio or Array Server...(1067)
--- Include duplicate reads in DNA-Seq data...(1062)
--- Understand Filter Ngs Files reports...(1043)
--- How is gene model used in RNA-Seq alignment...(1030)
--- Bas and BAM files...(1027)
--- Sharing project(s) using ArrayServer and ArrayViewer...(1026)
--- Manage Cloud Files...(1021)
--- Cloud error message: Not sufficient capacity in cloud...(1020)
--- SimulateQueue...(1005)
--- Getting downloading error when analyzing microarray data...(995)
--- Genome Browser Use Case: Access genome browser session via hyperlinks in an excel file...(992)
--- Hardware/software requirements for LandExplorer...(986)
--- Why I cannot zoom heatmap?...(967)
--- How can I connect data points from the same sample by lines in views?...(947)
--- CloudVolumeTag...(932)
--- Export Consensus Sequence...(910)
--- Interpret and visualize fusion report...(893)
--- How is pair information used in RNA-Seq alignment...(879)
--- Libgdiplus complie error...(874)
--- How to save filters and filtered data...(869)
--- How to make RNA-Seq gene ID recognized by MicroArray modules...(867)
--- Which columns will be indexed as ID for autofill in ArrayServer Search...(864)
--- "Could not find file" error...(859)
--- GSEA could not find buckets file...(859)
--- OncoLand Case Study - OncoGEO...(852)
--- How can I merge multiple projects into a single project in Array Studio?...(841)
--- Save Project After Each Important Step During Analysis...(832)
--- Why the .osreg files I put in Instruction folder are not processed?...(824)
--- SubnetID...(821)
--- Application validation did not succeed...(813)
--- Output all entries for a specific field...(808)
--- Array Studio IT Requirements...(791)
--- Change resolution of exported images...(789)
--- Paired-end reads filtering...(778)
--- CloudMaxInstanceCountPerJob...(753)
--- How to check the installation and enable .NET 3.5 in Windows...(750)
--- Revoke/unpublish a project from ArrayServer...(750)
--- Tips In Setting Up Oshell...(734)
--- Why do I see zero effective alignment counts after adding aligned BAM files...(731)
--- What does dot mean in variation report...(725)
--- Which algorithm / parameters are used in searching illumina adaptors sequences?...(721)
--- Ftpupload...(693)
--- Benchmark ArrayStudio to RStudio.pdf...(666)
--- Error: Timeout exceeded while waiting for welcome message...(664)
--- Cloud error message: Runtime was not set up for cloud file...(636)
--- Mageck Pscript demo.pdf...(621)
--- View alignments and reads in genome browser...(618)
--- Run jobs in local when you are in server project...(589)
--- What is the relationship between sampleset and project?...(582)
--- EnableAWSSpot...(564)
--- Genome Browser Share Options...(551)
--- Export powerpoint size is too small...(541)
--- Land Delivery error message: Cannot handle address family...(528)
--- How genes are prioritized in mutation annotation...(503)
--- Unable to install arraystudio due to security settings...(463)
--- Decryptcloud...(435)
--- Stack ovf guard base not met...(329)
--- Change Array Studio Omicsoft directory...(166)
--- CustomCommand...(50)


Back to Omicsoft KnowledgeBase

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