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bioc
NanoMethViz:Visualise methylation data from Oxford Nanopore sequencing
NanoMethViz is a toolkit for visualising methylation data from Oxford Nanopore sequencing. It can be used to explore methylation patterns from reads derived from Oxford Nanopore direct DNA sequencing with methylation called by callers including nanopolish, f5c and megalodon. The plots in this package allow the visualisation of methylation profiles aggregated over experimental groups and across classes of genomic features.
Maintained by Shian Su. Last updated 20 days ago.
softwarelongreadvisualizationdifferentialmethylationdnamethylationepigeneticsdataimportzlibcpp
26 stars 6.95 score 11 scriptsbioc
CytoGLMM:Conditional Differential Analysis for Flow and Mass Cytometry Experiments
The CytoGLMM R package implements two multiple regression strategies: A bootstrapped generalized linear model (GLM) and a generalized linear mixed model (GLMM). Most current data analysis tools compare expressions across many computationally discovered cell types. CytoGLMM focuses on just one cell type. Our narrower field of application allows us to define a more specific statistical model with easier to control statistical guarantees. As a result, CytoGLMM finds differential proteins in flow and mass cytometry data while reducing biases arising from marker correlations and safeguarding against false discoveries induced by patient heterogeneity.
Maintained by Christof Seiler. Last updated 5 months ago.
flowcytometryproteomicssinglecellcellbasedassayscellbiologyimmunooncologyregressionstatisticalmethodsoftware
2 stars 5.68 score 1 scripts 1 dependents
conig
corx:Create and Format Correlation Matrices
Create correlation (or partial correlation) matrices. Correlation matrices are formatted with significance stars based on user preferences. Matrices of coefficients, p-values, and number of pairwise observations are returned. Send resultant formatted matrices to the clipboard to be pasted into excel and other programs. A plot method allows users to visualize correlation matrices created with 'corx'.
Maintained by James Conigrave. Last updated 2 years ago.
5 stars 4.34 score 44 scriptsbioc
ScreenR:Package to Perform High Throughput Biological Screening
ScreenR is a package suitable to perform hit identification in loss of function High Throughput Biological Screenings performed using barcoded shRNA-based libraries. ScreenR combines the computing power of software such as edgeR with the simplicity of use of the Tidyverse metapackage. ScreenR executes a pipeline able to find candidate hits from barcode counts, and integrates a wide range of visualization modes for each step of the analysis.
Maintained by Emanuel Michele Soda. Last updated 5 months ago.
softwareassaydomaingeneexpressionhigh-throughput-screening
1 stars 3.11 score 13 scripts