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

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INPUT	OUTPUT

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

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OUTPUT

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

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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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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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Barplot of gene ontology analysis performed with the external tool Enrichr.

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

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Heatmap of expression values along cardiac differentiation of selected genes.

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MAploto of DEseq2 differential gene expression analysis in embryonic stem cells upon differentiation.

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

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PCA analysis in 3D of RNAseq experiments of embryonic stem cells to mesoderm precursors to cardiomyocytes upon differentiation.

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INPUT	OUTPUT

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

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Volcano plot of DESeq2 output from differential gene expression analysis of embryonic stem cells upon differentiation.

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INPUT	OUTPUT

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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INPUT	OUTPUT

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

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INPUT	OUTPUT

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

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INPUT	OUTPUT

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

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Pattern matching scanning of a regulatory sequence using position weight matrices.

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

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

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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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INPUT	OUTPUT