ISAnalytics 1.6.2
ISAnalytics is an R package developed to analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies.
ISAnalytics
can be installed quickly in different ways:
devtools
There are always 2 versions of the package active:
RELEASE
is the latest stable versionDEVEL
is the development version, it is the most up-to-date version where
all new features are introducedRELEASE version:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ISAnalytics")
DEVEL version:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("ISAnalytics")
RELEASE:
if (!require(devtools)) {
install.packages("devtools")
}
devtools::install_github("calabrialab/ISAnalytics",
ref = "RELEASE_3_15",
dependencies = TRUE,
build_vignettes = TRUE)
DEVEL:
if (!require(devtools)) {
install.packages("devtools")
}
devtools::install_github("calabrialab/ISAnalytics",
ref = "master",
dependencies = TRUE,
build_vignettes = TRUE)
ISAnalytics
has a verbose option that allows some functions to print
additional information to the console while they’re executing.
To disable this feature do:
# DISABLE
options("ISAnalytics.verbose" = FALSE)
# ENABLE
options("ISAnalytics.verbose" = TRUE)
Some functions also produce report in a user-friendly HTML format, to set this feature:
# DISABLE HTML REPORTS
options("ISAnalytics.reports" = FALSE)
# ENABLE HTML REPORTS
options("ISAnalytics.reports" = TRUE)
In the newer version of ISAnalytics, we introduced a “dynamic variables system”,
to allow more flexibility in terms of input formats. Before starting with the
analysis workflow, you can specify how your inputs are structured so that
the package can process them. For more information on how to do this
take a look at vignette("workflow_start", package = "ISAnalytics")
.
The first steps of the analysis workflow involve the import and parsing of data and metadata files from disk.
import_association_file()
and/or
import_Vispa2_stats()
import_single_Vispa2Matrix()
or
import_parallel_Vispa2Matrices()
Refer to the vignette
vignette("workflow_start", package = "ISAnalytics")
for
more details.
ISAnalytics offers several different functions for cleaning and pre-processing your data.
compute_near_integrations()
outlier_filter()
remove_collisions()
, see also the dedicated vignette
vignette("workflow_start", package = "ISAnalytics")
purity_filter()
aggregate_values_by_key()
, aggregate_metadata()
, see also the
dedicated vignette
vignette("workflow_start", package = "ISAnalytics")
You can answer very different biological questions by using the provided functions with appropriate inputs.
sample_statistics()
compute_abundance()
, integration_alluvial_plot()
top_integrations()
top_targeted_genes()
CIS_grubbs()
,
CIS_volcano_plot()
gene_frequency_fisher()
, fisher_scatterplot()
, circos_genomic_density()
is_sharing()
, iss_source()
, sharing_heatmap()
,
sharing_venn()
HSC_population_size_estimate()
,
HSC_population_plot()
For more, please refer to the full function reference.
Several implemented functions produce static HTML reports that can be saved on disk, or tabular files. Reports contain the relevant information on how the function was called, inputs and outputs statistics, and session info for reproducibility.
ISAnalytics has it’s dedicated package website where you can browse the documentation and vignettes easily, in addition to keeping up to date with all relevant updates. Visit the website at https://calabrialab.github.io/ISAnalytics/
If you have any issues the documentation can’t solve, get in touch by opening an issue on GitHub or contacting the maintainers