- recipe bioconductor-bumhmm
Computational pipeline for computing probability of modification from structure probing experiment data
This is a probabilistic modelling pipeline for computing per- nucleotide posterior probabilities of modification from the data collected in structure probing experiments. The model supports multiple experimental replicates and empirically corrects coverage- and sequence-dependent biases. The model utilises the measure of a "drop-off rate" for each nucleotide, which is compared between replicates through a log-ratio (LDR). The LDRs between control replicates define a null distribution of variability in drop-off rate observed by chance and LDRs between treatment and control replicates gets compared to this distribution. Resulting empirical p-values (probability of being "drawn" from the null distribution) are used as observations in a Hidden Markov Model with a Beta-Uniform Mixture model used as an emission model. The resulting posterior probabilities indicate the probability of a nucleotide of having being modified in a structure probing experiment.
- package bioconductor-bumhmm¶
- depends bioconductor-biostrings:
- depends bioconductor-iranges:
- depends bioconductor-summarizedexperiment:
- depends r-base:
- depends r-devtools:
- depends r-gtools:
- depends r-stringi:
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-bumhmm and update with:: mamba update bioconductor-bumhmm
To create a new environment, run:
mamba create --name myenvname bioconductor-bumhmm
myenvnamebeing 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-bumhmm:<tag> (see `bioconductor-bumhmm/tags`_ for valid values for ``<tag>``)