Tutorials of SeqCode web tools

NGS Tools

TUTORIAL 1. Compare2Peaks

Compare the genome-wide distribution of peaks of two ChIPseq experiments in mESCs: H3K4me3 and H3K27me3 (bivalent domains).

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TUTORIAL 2. ComputeChIPlevels

Determine the count of normalized reads of the ChIPseq of H3K4me3 in mESCs for the full catalog of mouse genes stratified by expression.

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INPUTOUTPUT

TUTORIAL 3. PeakAnnotator

Distribution of gene categories for the set of regions encoding mouse genes in the chromosome 19.

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OUTPUT

TUTORIAL 4. ProduceGENEplots

Meta-gene plot of the ChIPseq of H3K4me3 in mESC for the full catalog of mouse genes stratified by expression.

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INPUTOUTPUT

TUTORIAL 5. ProduceTSSmaps

Heatmap of ChIPseq signal of H3K4me3/H3K36me3, RNA polymerase II (Ser5P/Ser2P) and IgG in mESCs for a set of genes.

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INPUTOUTPUT

TUTORIAL 6. ProduceTSSplots

Aggregated plot of the ChIPseq of H3K4me3 in mESC around the TSS of the full catalog of mouse genes stratified by expression.

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Data Sets

TUTORIAL 7. BoxPlotter

Boxplot of expression values in three conditions along cardiac cell differentiation for mesdomerm markers and pairwise statistical test analyses.

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TUTORIAL 8. BoxPlotter2

Boxplot of expression in cardiomyocytes of multiple groups of developmental marker genes.

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TUTORIAL 9. BoxPlotter3

Boxplot of expression of pluripotency gene markers along several time points of cardiac differentiation.

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TUTORIAL 10. HeatMapper

Heatmap of expression values along cardiac differentiation of selected genes.

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TUTORIAL 11. PCAplotter

PCA analysis of eight RNAseq experiments in duplicates for embryoid bodies that are differentiated.

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TUTORIAL 12. ScatterPlotter

Scatterplot of gene expression values for the whole genome, highlighting pluripotency markers and housekeeping genes.

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Data Sets

TUTORIAL 13. AlluvialPlotter

Alluvial diagram that shows the relationships between H3K4me3, H3K27me3, H3K36me3, Ring1b and Suz12 (mouse ESCs) in the full set of 24508 genes (mm9).

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TUTORIAL 14. Compare2Genes

Venn diagram that shows the overlap between H3K4me3 and H3K27me3 target genes (bivalent genes).

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TUTORIAL 15. UpSetPlotter

UpSet chart that displays distinct overlapping subsets of target genes of H3K4me3, H3K27me3, H3K36me3 and RNA polymerase II modifications.

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TUTORIAL 16. VennPlotter

Venn diagram that displays distinct overlapping subsets of target genes of H3K4me3, H3K27me3, H3K36me3 and RNA polymerase II modifications.

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INPUTOUTPUT

Data Sets

TUTORIAL 17. FCanalysis

Determination of the list of genes up- and down-regulated between ESC and cardiomyocytes (RNAseq expression).

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TUTORIAL 18. FilterValues

Looking for highly expressed genes in ESC that are moderately expressed in cardiomyocytes.

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TUTORIAL 19. Join2Lists

Using the file of expression values for all the genes in the mouse genome, extract the values for a subset of genes.

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