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bioc
TREG:Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data
RNA abundance and cell size parameters could improve RNA-seq deconvolution algorithms to more accurately estimate cell type proportions given the different cell type transcription activity levels. A Total RNA Expression Gene (TREG) can facilitate estimating total RNA content using single molecule fluorescent in situ hybridization (smFISH). We developed a data-driven approach using a measure of expression invariance to find candidate TREGs in postmortem human brain single nucleus RNA-seq. This R package implements the method for identifying candidate TREGs from snRNA-seq data.
Maintained by Louise Huuki-Myers. Last updated 3 months ago.
softwaresinglecellrnaseqgeneexpressiontranscriptomicstranscriptionsequencingbioconductordeconvolutionrnascopescrna-seqsmfishsnrna-seqtreg
11.5 match 4 stars 5.20 score 5 scripts
cran
smfishHmrf:Hidden Markov Random Field for Spatial Transcriptomic Data
Discovery of spatial patterns with Hidden Markov Random Field. This package is designed for spatial transcriptomic data and single molecule fluorescent in situ hybridization (FISH) data such as sequential fluorescence in situ hybridization (seqFISH) and multiplexed error-robust fluorescence in situ hybridization (MERFISH). The methods implemented in this package are described in Zhu et al. (2018) <doi:10.1038/nbt.4260>.
Maintained by Qian Zhu. Last updated 4 years ago.
1.6 match 1.70 score