recipe bioconductor-tloh

Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/tLOH.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-tloh/meta.yaml

tLOH, or transcriptomicsLOH, assesses evidence for loss of heterozygosity (LOH) in pre-processed spatial transcriptomics data. This tool requires spatial transcriptomics cluster and allele count information at likely heterozygous single-nucleotide polymorphism (SNP) positions in VCF format. Bayes factors are calculated at each SNP to determine likelihood of potential loss of heterozygosity event. Two plotting functions are included to visualize allele fraction and aggregated Bayes factor per chromosome. Data generated with the 10X Genomics Visium Spatial Gene Expression platform must be pre-processed to obtain an individual sample VCF with columns for each cluster. Required fields are allele depth (AD) with counts for reference/alternative alleles and read depth (DP).

package bioconductor-tloh

versions:

1.10.0-0,  1.8.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-matrixgenerics:

>=1.14.0,<1.15.0

depends bioconductor-variantannotation:

>=1.48.0,<1.49.0

depends r-base:

>=4.3,<4.4.0a0

depends r-bestnormalize:

depends r-data.table:

depends r-depmixs4:

depends r-dplyr:

depends r-ggplot2:

depends r-naniar:

depends r-purrr:

depends r-scales:

depends r-stringr:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-tloh

and update with::

   mamba update bioconductor-tloh

To create a new environment, run:

mamba create --name myenvname bioconductor-tloh

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-tloh:<tag>

(see `bioconductor-tloh/tags`_ for valid values for ``<tag>``)

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