tomoseqr

tomoseqr is an R package for analyzing Tomo-seq (a method to obtain genome-wide expression data with spatial resolution) data. The algorithm of image reconstruction is based on Junker et al, 2014.

Detailed manual

Detailed manual is available at https://bioconductor.org/packages/release/bioc/vignettes/tomoseqr/inst/doc/tomoseqr.html

Usage

Installation

From Bioconductor

if (!require("BiocManager"))
    install.packages("BiocManager")

BiocManager::install("tomoseqr")

From Github

library(devtools)
install_github("bioinfo-tsukuba/tomoseqr")

Data preparation

Please prepare Tomo-seq data that meets the following requirements.

It is a data.frame object for each axis.
Its first cloumn has gene ID. It’s not enough that only row names indicate gene ID.
The order of the second and subsequent columns should be the same as the order of the sections.
It has a header.

Data example

  gene_ID   section1 section2   section3   section4
1   gene1   0.000000   0.0000 2867.75420 9086.81135
2   gene2 440.599448 531.7915   36.91591  484.06813
3   gene3  75.446821 833.9432  736.82367  559.89157
4   gene4 506.865166 930.0414  880.26654   52.85974
5   gene5   2.159842 271.6788  210.06446  445.08979

Example usage

library(tomoseqr)
data("testx", "testy", "testz", "mask")
tomoObj <- estimate3dExpressions(
    testx,
    testy,
    testz,
    mask = mask,
    query = c("gene1", "gene2", "gene3")
)
imageViewer(tomo_obj)

example

Reference

Junker et al. Genome-wide RNA Tomography in the Zebrafish Embryo. Cell, 2014.
https://doi.org/10.1016/j.cell.2014.09.038

Contact

Ryosuke Matsuzawa / shingenmochi