In mashranga/MolDia: Single cell In-Situ sequencing (ISS) data analysis

MolDia

Package description : R package to analyze single cell in-situ sequencing (ISS) data

Install package

install.packages("devtools")
library(devtools)
install_github("mashranga/MolDia")

Scope of the package

The scope of the package can be devided into following broad category

General structure of MolDia object

1. RCA_class : Main object definition and structure of "RCA_class" of MolDia package

Default example data-set

1. marker_gene: Neuronal marker gene by group

Read, manipulateand filter RCA ISS data

Read data

1. readRCA : Function to read RCA ISS data. THis function has different parameter, how to read and what to read. See detail in function help.
2. ISS_rotate : Rotate a tissue by specific angle or flip by x or y axis.

Filter data

1. RCA_barplot: Plot bar plot on RCA data bsed on different condition. In general filter data set based on different gese condition.
2. RCA_filter: Filter RCA data based on poisson distibution (Experimental)

Region of interest

1. RCA_GridSelect: Draw and Select grid of interest from a tissue

ISS data summary and vizualization

1. genesSummary: Summary of Specific gene of interest in ISS data. This include percentage of gene of interest positive cell with their distribution in other positive cells and visa-versa.
2. readsSummary: Summary of RCA data
3. ISS_pieplot: Venn-pie chart on ISS data based on genes of interest
4. RCA_map: Map ISS data based on different feature like cell, gene, cluster, tSNE

Multiple ISS data comparision

1. ISS_compare: Relation of multiple ISS data interms of total reads per gene. The result is presented in fitted regression line with R^2.
2. ISS_ratiocor: Calculate and plot correlation and ratio of total reads between genes by concedering group of tissue.

ISS data dimention reduction

1. RCA_tsne: Any data in class RCA_class clusteded or not clustered used to reduce dimention to 2D by RCA-tsne.

ISS data preprocessing

1. RCA_preprocess: Pre-process RCA data interms of normalization, scalling and centering

ISS clustering

Cluster

1. RCA_cluster: Cluster in-situ RCA data by different methods
2. RCA_ClusterSelect : Select cluster of interest after clustering
3. RCA_spatial : ISS spatial clustering (Experimental)

Cluster marker

1. RCA_marker: Find Cluster marker of in-situ RCA data and plot significant gene cluster wise by barplot and heatmap.

Cluster compare

1. RCA_clustcompare: Compare cluster of two tissue and find their similarity by Random forest algorithm.

Differentially express gene

1. RCA_DE: Find differentially express gene by different methods

Need to updrade

1. In function RCA_map plot empty cells foe specific genes.
2. legend problem In function RCA_map plot
3. Add violon plot in function RCA_map
4. Add tsne subplot for selected gene

mashranga/MolDia documentation built on May 26, 2019, 9:36 a.m.