The High Throughput Sequencing Cell Authentication Toolkit (seqCAT) is an R-package for authenticating, evaluating and characterisation of cells using single nucleotide variants (SNVs) from sequencing data. Its input data should be on the form of VCF files, i.e. output from variant callers such as the Genome Analysis ToolKit and annotated with software such as SnpEff.
seqCAT package is available on both Bioconductor and here on
GitHub. You can install the latest, stable version from Bioconductor like so:
# install.packages("BiocManager") BiocManager::install("seqCAT")
If you are interested in the development version of
seqCAT, you can install
it from GitHub:
# install.packages("devtools") devtools::install_github("fasterius/seqCAT")
You may also install
seqCAT using Conda:
conda install -c bioconda bioconductor-seqcat
To list the versions of
seqCAT available on Conda, you can use the
conda search -c bioconda bioconductor-seqcat
The general workflow of
seqCAT consists of three steps:
1. Creation of SNV profiles 2. Comparisons of SNV profiles 3. Evaluation of profile comparisons
# Load the package library("seqCAT") # Path to the example VCF file vcf <- system.file("extdata", "example.vcf.gz", package = "seqCAT") # Create SNV profiles hct116 <- create_profile(vcf, "HCT116") hke3 <- create_profile(vcf, "HKE3") rko <- create_profile(vcf, "RKO") # Compare all profiles to each other profiles <- list(hct116, hke3, rko) comparisons <- compare_many(profiles) # Create an heatmap of comparisons and their similarity scores plot_heatmap(comparisons[])
For more detailed instructions on how to use
seqCAT, please see the
If you are using
seqCAT to analyse your data, please cite the
seqCAT: a Bioconductor R-package for variant analysis of high throughput sequencing data Fasterius E. and Al-Khalili Szigyarto C. F1000Research (2018), 7:1466 https://f1000research.com/articles/7-1466
seqCAT package is released with a MIT licence and is a free software: you
may redistribute and/or modify it under the terms of the license. For more
information, please see the
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