Man pages for mashranga/MolDia
Single cell In-Situ sequencing (ISS) data analysis
| exportISS | Export ISS data in different formated file. |
| ISS_barplot | Plot barplot on ISS data bsed on different condition |
| ISS_clustCompare | Compare among ISS clusters based on Random Forest algorithm |
| ISS_cluster | Cluster ISS data based on different methods. |
| ISS_cluster_seruat | "ISS_cluster_seruat" Cluster ISS data by SEURAT. |
| ISS_cluster_spatial | Spatial clustering for ISS by Markov random field model. |
| ISS_clustMarker | Find Cluster marker of ISS data. |
| ISS_clustSelect | Select cluster of interest after clustering. |
| ISS_compare | Compare multiple ISS data based on gene |
| ISS_deg | Find differentially express (DE) gene by different methods |
| ISS_filter | Filter ISS data based on poisson distibution |
| ISS_genesSummary | Summary of specific gene of interest in ISS data |
| ISS_map | Plot function for MolDiaISS data. |
| ISS_pca | Principle component analyis on ISS data |
| ISS_pieplot | Venn-pie chart on ISS data based on genes of interest |
| ISS_preprocess | Preprocess ISS data based on different normalization method. |
| ISS_ratiocor | Calculate and plot correlation and ratio of total reads... |
| ISS_readsSummary | Summary of ISS data and expression |
| ISS_roi | Select grid/region of interest (ROI) from a tissue. |
| ISS_rotate | Rotate and flip ISS data |
| ISS_sumstat | Calculate summary statstics of data |
| ISS_tsne | Dimentionality reduction to 2D by tSNE |
| marker_gene | Gene set for neuronal marker |
| MolDiaISS | The ISS data class for segmentated file |
| MolDiaISS_nonsegment | The ISS data class for non-segmentated file |
| readISS | Read ISS data |
| single_cell | Single cell RNA seq data |
| writeISS | Write ISS data in CSV formate |
