Hydra vulgaris Genome
READ ME
Using the tabs at the top, users can explore the following information:
Cell Info vs Gene Expression, Cell Info vs. Cell
Info, Gene Expression vs. Gene Expression, Gene Coexpression, Violin Plot/Box Plot,
Bubble Plot/ Heat map, Funtional Annotations and Conversion tables.
To use these tabs, the user selects
the desired dimension reduction for the X- and Y-axes using the drop down menu. For
cell information, users can visualize cell types or library batches using the drop down menu. For gene
expression information, users can visualize genes of interest by exploring the drop
down menu or typing in their gene of interest. Gene expression is colored in a
White-Red color scheme which can be changed in the plot controls (see Advanced Options section).
To use these tabs, the user selects
the desired dimension reduction for the X- and Y-axes using the drop down menu. For
cell information, users can visualize cell types or library batches using the drop down menu. Categorical
covariates have a fixed color palette while continuous covariates are colored in a
Blue-Yellow-Red color scheme which can be changed in the plot controls (see Advanced Options section).
To use these tabs, the user selects
the desired dimension reduction for the X- and Y-axes using the drop down menu. For gene
expression information, users can visualize genes of interest by exploring the drop
down menu or typing in their gene of interest. Gene expression is colored in a
White-Red color scheme which can be changed in the plot controls (see Advanced Options section).
To use these tabs, the user selects, the desired dimension reduction for the X- and Y-axes using the drop down menu.
For gene expression information, users can visualize genes of interest by exploring the drop
down menu or typing in their genes of interest. For Gene 1, gene expression are colored in a
White-Red color scheme which can be changed in the plot controls (see Advanced Options)
For Gene 2, gene expression are colored in a
White-Blue color scheme which can be changed in the plot controls (see Advanced Options).
Cells where genes are coexpressed will be colored in purple/pink which can be changed in the
plot controls (see Advanced Options).
Insert directions here.
Insert directions here.
Overview
The adult Hydra polyp continuously renews all of its cells using three separate stem cell populations, but the genetic pathways enabling this homeostatic tissue maintenance are not well understood. We used Drop-seq to sequence the transcriptomes of 24,985 single Hydra cells to uncover the molecular signatures of a broad spectrum of cell states, from stem cells to terminally differentiated cells. This portal presents these data in an interactive format, and allows for visualization of sequencing statistics, clustering results, and gene expression across every cell in our dataset.How to use this portal
Using the tabs at the top, users can explore the following information:
Cell Info vs Gene Expression, Cell Info vs. Cell
Info, Gene Expression vs. Gene Expression, Gene Coexpression, Violin Plot/Box Plot,
Bubble Plot/ Heat map, Funtional Annotations and Conversion tables.
CellInfo vs GeneExpr
Cell information vs gene expression on dimension reduction
In this tab, users can visualise both cell information and gene expression side-by-side on low-dimensional representations.
To use these tabs, the user selects
the desired dimension reduction for the X- and Y-axes using the drop down menu. For
cell information, users can visualize cell types or library batches using the drop down menu. For gene
expression information, users can visualize genes of interest by exploring the drop
down menu or typing in their gene of interest. Gene expression is colored in a
White-Red color scheme which can be changed in the plot controls (see Advanced Options section).
CellInfo vs CellInfo
Cell information vs cell information on dimension reduction
In this tab, users can visualise two cell informations side-by-side on low-dimensional representations.
To use these tabs, the user selects
the desired dimension reduction for the X- and Y-axes using the drop down menu. For
cell information, users can visualize cell types or library batches using the drop down menu. Categorical
covariates have a fixed color palette while continuous covariates are colored in a
Blue-Yellow-Red color scheme which can be changed in the plot controls (see Advanced Options section).
GeneExpr vs GeneExpr
Gene expression vs gene expression on dimension reduction
In this tab, users can visualise two gene expressions side-by-side on low-dimensional representations.
To use these tabs, the user selects
the desired dimension reduction for the X- and Y-axes using the drop down menu. For gene
expression information, users can visualize genes of interest by exploring the drop
down menu or typing in their gene of interest. Gene expression is colored in a
White-Red color scheme which can be changed in the plot controls (see Advanced Options section).
Gene coexpression
Coexpression of two genes on reduced dimensions
In this tab, users can visualise the coexpression of two genes on low-dimensional representions.
To use these tabs, the user selects, the desired dimension reduction for the X- and Y-axes using the drop down menu.
For gene expression information, users can visualize genes of interest by exploring the drop
down menu or typing in their genes of interest. For Gene 1, gene expression are colored in a
White-Red color scheme which can be changed in the plot controls (see Advanced Options)
For Gene 2, gene expression are colored in a
White-Blue color scheme which can be changed in the plot controls (see Advanced Options).
Cells where genes are coexpressed will be colored in purple/pink which can be changed in the
plot controls (see Advanced Options).
Violinplot / Boxplot
Cell information / gene expression violin plot / box plot
In this tab, users can visualise the gene expression or continuous cell information (e.g. Number of UMIs / module score) across groups of cells (e.g. libary / clusters).
Insert directions here.
Bubbleplot / Heatmap
Gene expression bubbleplot / heatmap
In this tab, users can visualise the gene expression patterns of multiple genes grouped by categorical cell information (e.g. library / cluster). The normalised expression are averaged, log-transformed and then plotted.
Insert directions here.
Functional Annotations
Conversion Table
CellInfo vs GeneExpr
Cell information vs gene expression on reduced dimensions
In this tab, users can visualise both cell information and gene expression side-by-side on low-dimensional representions.Dimension Reduction
CellInfo vs CellInfo
Cell information vs cell information on dimension reduction
In this tab, users can visualise two cell informations side-by-side on low-dimensional representions.Dimension Reduction
GeneExpr vs GeneExpr
Gene expression vs gene expression on dimension reduction
In this tab, users can visualise two gene expressions side-by-side on low-dimensional representions.Dimension Reduction
Gene coexpression
Coexpression of two genes on reduced dimensions
In this tab, users can visualise the coexpression of two genes on low-dimensional representions.Dimension Reduction
Violinplot / Boxplot
Cell information / gene expression violin plot / box plot
In this tab, users can visualise the gene expression or continuous cell information (e.g. Number of UMIs / module score) across groups of cells (e.g. libary / clusters).
Bubbleplot / Heatmap
The normalised expression are averaged, log-transformed and then plotted.
Gene expression bubbleplot / heatmap
In this tab, users can visualise the gene expression patterns of multiple genes grouped by categorical cell information (e.g. library / cluster).The normalised expression are averaged, log-transformed and then plotted.
Functional Annotations
Conversion Table
This webpage was made using ShinyCell