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.
library(devtools)
install_github("bioinfo-tsukuba/tomoseqr")
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.
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
library(tomoseqr)
data("testx", "testy", "testz", "mask")
tomo_obj <- Estimate3dExpressions(
testx,
testy,
testz,
mask=mask,
query=c("gene1", "gene2")
)
ImageViewer(tomo_obj, "gene1")
Animate2d(tomo_obj, "gene1", target="unite")
Junker et al. Genome-wide RNA Tomography in the Zebrafish Embryo.
Cell, 2014.
https://doi.org/10.1016/j.cell.2014.09.038
Ryosuke Matsuzawa / shingenmochi