RNA sequencing
calcnormfactors operator
Description
calcnormfactors
operator calculates a normalization factor per column (i.e sample).
Usage
Input projection | . |
---|---|
row |
represents the genes |
col |
represents the samples |
y-axis |
is the input data for which to compute the normalization factor |
Output relations | . |
---|---|
normfactor |
numeric, per column (i.e. per sample) |
Details
The operator is the calcnormfactor in the edgeR bioconductor.
References
see the edgeR
R package for the documentation.
See Also
Examples
GitHub link
DESeq2_two_conditions operator
Description
DESeq2_two_conditions
tests for differential gene expression in samples from two conditions using the DESeq2
package from BioConductor (Love, et al, Genome Biology, 2014).
Usage
Input projection | Description |
---|---|
row |
Gene name/identifier |
column |
Sample name/identifier |
color |
Represents the groups to compare |
y-axis |
Sequence counts |
Input parameters | Description |
---|---|
alpha |
Numeric, adjusted p value cutoff for independent filtering (default = 0.1) |
LFC_shrinkage |
Logical, whether the returned log fold-change values should be shrinked (default = TRUE) |
shrinkage_type |
“normal”, “apeglm” or “ashr”, Type of shrinkage estimator to use (default = “normal”) |
Output relations | Description |
---|---|
pvalue |
numeric, p-value calculated per gene |
padj |
numeric, p-value calculated per gene after adjusting for multiple testing |
baseMean |
numeric, mean of normalized counts for all the samples |
log2FoldChange |
numeric, shrunken log2 fold-change between the two groups to compare |
minus_log10_padj |
numeric, negative log10 transformation of padj for more intuitive plotting |
Details
The operator uses the DESeq2
package from BioConductor.
References
Love MI, Huber W, Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, 550. doi: 10.1186/s13059-014-0550-8.
See “Analyzing RNA-seq data with DESeq2” for further information on DESeq2 by Love, et al.
GitHub link
diffcyt operator
Description
diffcyt
operator a differential analysis of flow cyto data and indicates which marker and cluster combinations are relevant.
Usage
Input projection | . |
---|---|
col |
group_id , patient_id |
row |
marker_class , marker_name |
y-axis |
values representing measurement |
Input parameters | . |
---|---|
analysis_type |
can be either DA (Differential Abundance) or DS (Differential State) |
Output relations | . |
---|---|
cluster_id |
character, cluster name, per cluster, DA and DS output |
LogFC |
numeric, log fold change, per cluster, DA |
LR |
numeric, lr, per cluster, DA output |
p_val |
numeric, p value, per cluster, DA output |
p_adj |
numeric, adjusted p value, per cluster, DA output |
LogFC |
numeric, log fold change, per cluster-marker, DS output |
p_val |
numeric, p value, per cluster-marker, DS output |
p_adj |
numeric, adjusted p value, per cluster-marker, DS output |
t |
numeric, t, per cluster-marker, DS output |
B |
numeric, B, per cluster-marker, DS output |
AvgExp |
numeric, adjusted p value, per cluster-marker, DS output |
Details
Performs differential analysis (abundance or state). See the diffcyt::diffcyt
function in the Bioconductor R pacakge.
References
see the github for documentation, https://github.com/lmweber/diffcyt
Examples
GitHub link
fgsea operator
Description
fgsea
operator performs a fast gene set enrichment analysis.
Usage
Input projection | . |
---|---|
y-axis |
numeric, input data usually a ranking statistics, per cell |
Output relations | . |
---|---|
NES |
numeric, fgsea of the input data |
padj |
numeric, adjusted p-value |
Details
The operator takes all the values of a cell and returns the value which is the fgsea. The computation is done per cell. There is one value returned for each of the input cell.
References
See Also
Examples
GitHub link
FlowSOM tuning operator
Description
flowsomtuning
operator performs flowSOM clustering for different numbers of clusters.
Usage
Input projection | . |
---|---|
row |
represents the variables (e.g. channels, markers) |
col |
represents the clusters (e.g. cells) |
y-axis |
is the value of measurement signal of the channel/marker |
Input parameters | . |
---|---|
min_cluster_number |
Minimum number of clusters to make |
max_cluster_number |
Maximal number of clusters to make |
transform |
Transform data? |
seed |
Random seed |
Output relations | . |
---|---|
cluster |
character, cluster label |
Details
The operator is a wrapper for the FlowSOM
function of the FlowSOM
R/Bioconductor package.
References
GitHub link
umap operator
Description
umap
operator performs umap analysis.
Usage
Input projection | . |
---|---|
row |
represents the variables (e.g. genes, channels, markers) |
col |
represents the observations (e.g. cells, samples, individuals) |
y-axis |
measurement value |
Input parameters | . |
---|---|
init |
character, type of initialization for the coordinates, see details |
scale |
numeric, type of scaling to apply to data |
spread |
numeric, the effective scale of embedded points. In combination with min_dist , this determines how clustered/clumped the embedded points are |
min_dist |
numeric, the effective minimum distance between embedded point |
pca |
numeric, If set to a positive integer value, reduce data to this number of columns using PCA |
Output relations | . |
---|---|
umap01, umap02 |
first two components containing the new projected values |
Details
The operator performs umap analysis. It reduces the amount of variables (i.e. indicated by rows) to a lower number (default 2). This operators wraps the uwot::umap()
. See (https://github.com/jlmelville/uwot) for more details, especially settings and examples.
Reference
Examples
GitHub link
vsn operator
Description
vsn
operator performs a normalization factor per column (i.e. sample).
Usage
Input projection | . |
---|---|
row |
represents the genes |
col |
represents the samples |
y-axis |
is the input data for which to normalization |
Output relations | . |
---|---|
norm |
numeric, the normalized values of the measurements (i.e. of each sample) |
Details
The operator is the justvsn
function from the VSN bioconductor package.
References
see the vsn
R package for the documentation.