Patch-seq is powerful technique that allows for multimodal characterization of individual neurons – electrophysiological, morphological and transcriptomic. At the Allen Institute we have optimized this technique to efficiently collect high-quality data. On this GitHub repo we provide links to the manuscript describing this optimized technique and associated data, a detailed protocol, Allen Institute manuscripts that have utilized this technique, and links to Allen Institute resources and software. In addition, this repo includes an R package of Patch-seq tools for quality control and cell typing of Patch-seq cells.
https://www.protocols.io/view/patch-seq-recording-and-extraction-detailed-protoc-bw6gphbw
https://elifesciences.org/articles/65482
https://github.com/AllenInstitute/MIES
Mouse Visual Cortex https://www.sciencedirect.com/science/article/pii/S009286742031254X
Human L2/3 - https://www.nature.com/articles/s41586-021-03813-8
Morpho-Electric database http://celltypes.brain-map.org/
Single-cell RNA-seq database https://portal.brain-map.org/atlases-and-data/rnaseq
Patch-Seq database of cells in mouse VISp is now available on Allen Brain Map.
R functions for gene selection and analysis of Patch-seq data.
patchseqtools includes several functions that are used for quality control and cell typing of Patch-seq cells at the Allen Institute. Many of these functions are wrappers for functions from other libraries (see below) and we enourage proper citation of relevant tools when using those functions.
Specific topics include:
- Assigning quality scores to each cell (mostly wrapper functions for https://github.com/PavlidisLab/patchSeqQC)
- Cell type clustering using CCA (mostly wrapper functions for https://satijalab.org/seurat/Seurat_AlignmentTutorial.html)
devtools::install_github("AllenInstitute/patchseqtools")
No vignettes currently available.
The license for this package is available on Github at: https://github.com/AllenInstitute/patchseqtools/blob/master/LICENSE
We are not planning to update the R library component of this repo unless bugs are found. We may make occasional updates to other components of the repository with no fixed schedule. However, we welcome community input through both issues and pull requests.
If you contribute code to this repository through pull requests or other mechanisms, you are subject to the Allen Institute Contribution Agreement, which is available in full at: https://github.com/AllenInstitute/patchseqtools/blob/master/CONTRIBUTION