Importing Package | Introduction | Installation | Bioconductor | Github | Analysis | Loading the package | Read Data | Object Creation | Removing all zero rows | Computing the needed tables | Quality Check | Mapped Reads | Density plot | Barcode Lost | Plot MDS | For Sample | For Treatment | For Day | Statistical Analysis | Z-score hit | CAMERA | ROAST | Find Common Hit | Plot common hit
Package: ScreenR 1.15.1
Emanuel Michele Soda
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.
Authors:
ScreenR_1.15.1.tar.gz
ScreenR_1.15.1.zip(r-4.7-any)ScreenR_1.15.1.zip(r-4.6-any)ScreenR_1.15.1.zip(r-4.5-any)
ScreenR_1.15.1.tgz(r-4.6-any)ScreenR_1.15.1.tgz(r-4.5-any)
ScreenR_1.15.1.tar.gz(r-4.7-any)ScreenR_1.15.1.tar.gz(r-4.6-any)
ScreenR_1.15.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ScreenR/json (API)
| # Install 'ScreenR' in R: |
| install.packages('ScreenR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/emanuelsoda/screenr/issues
Pkgdown/docs site:https://emanuelsoda.github.io
Datasets:
- annotation_table - Table for the annotation of Barcode
- count_table - Table of the count table
On BioConductor:ScreenR-1.15.0(bioc 3.24)ScreenR-1.14.0(bioc 3.23)
softwareassaydomaingeneexpressionhigh-throughput-screening
Last updated from:33390e9609. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 151 | ||
| linux-devel | NOTE | 250 | ||
| source / vignettes | OK | 223 | ||
| linux-release | NOTE | 273 | ||
| macos-release | NOTE | 268 | ||
| macos-oldrel | NOTE | 342 | ||
| windows-devel | NOTE | 212 | ||
| windows-release | NOTE | 222 | ||
| windows-oldrel | NOTE | 182 | ||
| wasm-release | OK | 102 |
Exports:barcode_lostcompute_data_tablecompute_explained_variancecompute_metricscompute_slopecount_mapped_readscreate_edger_objcreate_screenr_objectfilter_by_slopefilter_by_variancefind_camera_hitfind_common_hitfind_roast_hitfind_robust_zscore_hitfind_zscore_hitget_annotation_tableget_count_tableget_data_tableget_groupsget_normalized_count_tableget_replicatesmapped_readsnormalize_dataplot_barcode_hitplot_barcode_lostplot_barcode_lost_for_geneplot_barcode_trendplot_boxplotplot_common_hitplot_explained_varianceplot_mapped_readsplot_mapped_reads_distributionplot_mdsplot_trendplot_zscore_distributionremove_all_zero_rowset_annotation_tableset_count_tableset_data_tableset_groupsset_normalized_count_tableset_replicates
Dependencies:clicpp11dplyredgeRfarvergenericsggplot2ggvenngluegtableisobandlabelinglatticelifecyclelimmalocfitmagrittrpatchworkpillarpkgconfigpurrrR6RColorBrewerrlangS7scalesstatmodstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Table for the annotation of Barcode | annotation_table |
| Count number of barcode lost | barcode_lost |
| Compute data Table | compute_data_table |
| Compute Metrics | compute_metrics |
| Compute Slope of a Gene | compute_slope |
| Count the number of mapped read | count_mapped_reads |
| Table of the count table | count_table |
| Create edgeR Object | create_edger_obj |
| Create the ScreenR Object | create_screenr_object |
| Filter using the slope filter | filter_by_slope |
| Filter using the variance filter | filter_by_variance |
| Find Camera Hit | find_camera_hit |
| Find common hit | find_common_hit |
| Find Roast Hit | find_roast_hit |
| Title Find robust Z-score Hit | find_robust_zscore_hit |
| Title Find Z-score Hit | find_zscore_hit |
| Get ScreenR annotation table | get_annotation_table get_annotation_table,screenr_object get_annotation_table,screenr_object-method |
| Get ScreenR count table | get_count_table get_count_table,screenr_object get_count_table,screenr_object-method screenr_object screenr_object-class |
| Get ScreenR data_table | get_data_table get_data_table,screenr_object get_data_table,screenr_object-method |
| Get ScreenR groups | get_groups get_groups,screenr_object get_groups,screenr_object-method |
| Get ScreenR normalized_count_table | get_normalized_count_table get_normalized_count_table,screenr_object get_normalized_count_table,screenr_object-method |
| Get ScreenR replicates | get_replicates get_replicates,screenr_object get_replicates,screenr_object-method |
| Mapped Reads | mapped_reads |
| Normalize data | normalize_data |
| Plot barcode hit | plot_barcode_hit |
| Plot number of barcode lost | plot_barcode_lost |
| Plot number of barcode lost for gene | plot_barcode_lost_for_gene |
| Plot the trend over time of the barcodes | plot_barcode_trend |
| Plot Barcodes Hit | plot_boxplot |
| Plot common hit | plot_common_hit |
| Plot the explained variance by the PC | plot_explained_variance |
| Plot mapped reads | plot_mapped_reads |
| Plot the distribution of the mapped reads | plot_mapped_reads_distribution |
| Multidimensional Scaling Plot | plot_mds |
| Plot the trend hit gene | plot_trend |
| Plot distribution Z-score | plot_zscore_distribution |
| Remove rows that have zero count in all samples | remove_all_zero_row |
| Set ScreenR annotation table | set_annotation_table set_annotation_table,screenr_object set_annotation_table,screenr_object-method |
| Set ScreenR count table | set_count_table set_count_table,screenr_object set_count_table,screenr_object-method |
| Set ScreenR data_table | set_data_table set_data_table,screenr_object set_data_table,screenr_object-method |
| Set ScreenR groups | set_groups set_groups,screenr_object set_groups,screenr_object-method |
| Set ScreenR normalized_count_table | set_normalized_count_table set_normalized_count_table,screenr_object set_normalized_count_table,screenr_object-method |
| Set ScreenR replicates | set_replicates set_replicates,screenr_object set_replicates,screenr_object-method |