Table 1.
Comparison of the functionalities among ISAnalytics and state of the art methods. The comparison highlights pros and cons of every package, divided by macro-areas (leftmost column) and specific functionality (second column on the left)
| Functionality | ISAnalytics | barcodetrackR | |
|---|---|---|---|
| Software | Release | R package published on Bioconductor | R package published on Bioconductor |
| Metadata and association files | Yes (extensive use, plus hypothesis driven approach) | Yes (embedded in SummarizedExperiment data structure) | |
| Maintenance | Yes (last commit 2022) | Yes (last commit 2021) | |
| Data import and pre-processing | Data import | Reads files, converts to tidy, additional operations. Supports automatic import of multiple files in parallel. | File reading external to package (base R), then conversion to SummarizedExperiment (sparse). No parallelization (one file at time). |
| Sequencing data filtering | Yes (by pool with stat) | No | |
| Data recalibration | Yes (with report) | No | |
| Collision detection and removal | Yes (with report) | No | |
| Abundance filtering | Yes | Yes | |
| Purity filtering | Yes | No | |
| Data Manipulation | Data aggregation | Yes (customizable and metadata driven) | No |
| Statistics | Descriptive statistics | Yes (plus custom with lambda functions) | Yes (only specific stats: diversity indexes included are the same as ISAnalytics) |
| Clonal Tracking | Abundance | Yes | Yes |
| Samples correlations and similarity | No | Yes | |
| Tracking of top n clones in time | Yes | Yes (plus heatmaps) | |
| Clonal distribution over time | Yes (alluvial plots - not restricted to plot over time) | Yes (area plots - restricted to use time points) | |
| Barcode presence in heatmap | No | Yes | |
| Lineage bias analysis | Yes (using sharing functions) | Yes | |
|
Tracking unique clones with heatmap
(either barcodes or ISs) |
No (data available, to plot with simple heatmap call) | Yes | |
| Choord diagram | No | Yes | |
| CIS statistics | Yes (and with plots) | No | |
| Clonal sharing and waves of clones over time | Yes | No | |
| HSPC population size estimate | Yes | No | |
| Circos genomic density | Yes | No | |
| Reproducibility and human interaction | Interactive reports | Yes | No |
| Shiny interface | Yes | Yes |