FAQ       Help      Search   |   Browse       Qlucore Cloud hub and Web Cloud requirements Cloud solution Qlucore Licenses Change user License Server not found License Server Troubleshooting Move a license Product Versions Qlucore Omics Explorer Cloud packages Crashes in version 3.3 and onwards on some Dell computers Directional t-test and two group comparison Download trial File extensions How are counts counted when importing bam files? How to use correlation Multi group comparison and ANOVA Using remote connection to run Qlucore Omics Explorer   Analysis 2D PCA plot 2-way or two-way Anova Absent/present calls Anova in Qlucore BAM file sort order Biomarker Workbench Calculation of Fold change and Difference ChIP-seq and ATAC-seq Computation of R/R2 statistics Create a subset of variables based on PCA and use it to model. dCT values DESeq2 Distances Eliminate the time factor in data recorded at several time points Experiment designs (ANOVA, t-test, limma,...) Few or limited number of samples Find favorite genes, proteins or variables using the search function Fold change and difference Gene fusion analysis Hierarchial clustering algorithm Hierarchical clustering memory usage How do I know how much I should filter by variance or by statistical tests such as ANOVA How does Qlucore calculate the length of the gene to do the normalization? How is the z-score normalization (mean=0, Var=1) done in Qlucore Omics Explorer? Identifying subgroups, patterns and structure Linkage criterion Log functionality and logging analysis steps Low expression levels RNA-seq data filtering Methylation data support Missing values and reconstruction Most important PCA variables Network and graphs Normalization of RNAseq data in Qlucore Omics Explorer Normalization using housekeeping genes Normalization Z-score (mean=0, var=1) calculations Normalize RNA-seq data in R Normalizing PCR (QPCR or Q-PCR) data Open interface to R (API) Paired data Pathway analysis and gene sets Proteomic data analysis Quantile normalization and eliminated factors RNA-seq normalization for BAM files Selecting Affymetrix probesets using Jetset or collapse Single cell data analysis Statistical tests for the Extended option using the Open R API: Welch, Wilcoxon, Limma, Mann-Whitney Statistsics Supported classifier methods The signal-to-noise (SNR) metric Topological data analysis TPM values for RNASeq Two-color loop designs Unsupervised clustering Variable list and matches Variables differentiating and/or discriminating subgroups. Finding discrminating variables. Weighted correlation network analysis (WGCNA) What data is used in the Two group comparison (t-test) What is projection score and how do I use it. Working with multiple data sets (multi-omics) Working with RNA-seq data (bam)   Data Import 16S data Affymetrix Registration button not working Agilent arrays Analyze data from Array Express Analyzing Flow Cytometry data BAM file support for RNA-seq data. Convert from R to Qlucore data file format Data Import of file with multiple variable annotation columns Data pre-processing for expression data Data with many samples Decimal separator Error: The technology for the array type xxxxxxx can not be deducted Feature Extraction settings Gene lengths for count data How to download data from Gene Expression Omnibus (GEO) How to import 10X single cell data How to import data (RNA-seq, Illumina, Affymetrix, 10x, Agilent, Wizard, tab separated, csv, txt, bam) How To Import TCGA Data Import Affymetrix data Import Affymetrix microRNA and miRNA data Import and quantification of miRNA-seq data Import annotations Import of Illumina data Loading and creating annotations Manual import of data and annotations from GEO Normalization of imported RNA-seq data Out of memory when downloading CEL file annotations Save RNA-seq or Affymetrix files as .gedata Single Cell data in H5 format Supported data types These CHP files do not contain probeset IDs. Two colored arrays Use .sra files   NGS Module Biosulfite sequencing   Other 32 bit Windows operating systems Apple Mac Citing Qlucore Cloud Differences between Hierarchical clustering and PCA Export high resolution images for publications Export of images/videos Extended statistics and R Graphics issues and device drivers How do Qlucore Omics Explorer compares to R Mac OS RNAseq and array technologies System requirements Using Limma and Extended Statistics Using Tile (Ctrl+T) in Qlucore Omics Explorer cloud What is new in Qlucore Omics Explorer What is templates and how can it be used Windows Versions