Swan v3.2

• Fixed dependency issues

Swan v3.0

Swan 3.0

SwanGraph initialization

• Added bool options to SwanGraph initialization (edge_adata, end_adata, and ic_adata) that the user can set to False if they don't wish to track abundance for these individual transcript features

AnnData compatibility

• Allows for addition of abundance information directly from an AnnData object; bypassing dense-matrix representations of the data (SwanGraph.add_adata())

Documentation

• Updated sample data links
• Added AnnData data format to the file format specs
• Added additional examples to showcase functionality added in v3.0 and 2.5

Deprecation of differential gene and transcript expression tests

• Deprecated SwanGraph.de_gene_test() and SwanGraph.de_transcript_test() as I have not had luck running diffxpy in a while
• Added example tutorial on how to directly use a Swan AnnData to perform differential expression testing with PyDESeq2

Known issues

• Currently Cerberus does not output transcript novelty assignments to GTFs and they are therefore not parsed by Swan; will fix in a future update

swan v2.5

Swan 2.5

SwanGraph structure changes

• Counts and other expression structure (ie TPM, PI) are now stored as sparse matrices to massively save on on-disk as well as in-memory storage
• Capability of storing gene-level abundance information (SwanGraph.gene_adata) calculated separately from transcript-level
• Added AnnData to store intron chain level abundance information (SwanGraph.ic_adata)
• Added tracking for stable gene ID in cases where reference annotation versions don't match (ie ENSG000000014.5 --> ENSG000000014)

Native compatibility with cerberus transcriptomes

• Will track TSSs, ICs, and TESs called by cerberus based on the names of transcripts provided from the GTF

Other changes

• DIE test now reports top 2 DPI isoforms
• Faster counts and TPM calculations using Scanpy tools
• Added option to sort by isoform's cumulative PI value in the gene report sorting
• Added plotting option for plotting browser models directly on to a preexisting Matplotlib axis SwanGraph.plot_browser()
• Added plotting option to plot bed regions SwanGraph.pg.plot_regions()
• Added options to calculate TPM across multiple datasets as either the minimum or maximum of the values between the datasets

Minor bug fixes

• Fixed DIE test bug when there are >11 isoforms / gene
• Fixed bugs in SwanGraph.gen_report()

swan v2.0

Swan 2.0

General workflow update

• changed workflow from adding datasets / samples one at a time; now users can pass in one GTF with the union of all expressed transcripts in their data

SwanGraph representation updates

• removed strand from genomic location in SwanGraph.loc_df
• added strand to edges in SwanGraph.edge_df
• added AnnData representations for tracking transcript abundance as well as automatically-calculated edge, tss, and tes abundance
• added options to represent complex metadata in the AnnData.obs tables
• added a single-cell option to SwanGraph initialization for data with individual cells as samples
• automatically calculates percent isoform use (pi) per dataset per gene (except for in single-cell mode)
• added functions to add and store color palettes for different metadata colors

Analysis options update

• implemented more statistically-robust and published method of isoform switching testing (aka differential isoform expression [DIE] testing), as described by Joglekar et. al., 2021
• reworked differential gene and transcript expression testing to work smoothly with AnnData representation
• changed output type of intron retention / exon skipping analysis to be a more descriptive pandas DataFrame
• all analysis code will now automatically store results in the SwanGraph.adata.uns dictionary using an automatically-generated key that can be easily regenerated to facilitate different pairwise testing and accessing previous results

Gene report update

• removed indicate_dataset option
• added option to group datasets based on metadata columns (groupby)
• added option to include / exclude / order datasets based on metadata information (`datasets)
• added option to represent datasets using color coded bars either derived from the dataset names or metadata columns (metadata_cols), as well as draw a legend for the colors
• added option to either plot TPM or pi (layer)
• added option to change what color palette heatmap is plotted in (cmap)
• reworked options to indicate differentially-expressed transcripts in conjunction with how differential expression results are now stored (include_qvals, q, log2fc, qval_obs_col, qval_obs_conditions)
• added option to display values on top of each heatmap cell (display_numbers)
• added option to display transcript name as opposed to transcript ID

Other plotting changes

• removed indicate_dataset option
• added functions to change the colors of plotted Swan plots and browser plots

Other utilities

• added functions to output calculated edge, tss, or tes abundance along with details of genomic location
• added functions to calculate TPM or percent isoform use (pi) given specific metadata settings
• changed how SwanGraph saving and loading works

Note: Saved Swan objects that were generated with previous versions of Swan will not be compatible with 2.0!

swan v1.0.3

Fixes a missed dependency allowing for exon entries to be in whatever order beneath the corresponding transcript entries when loading from a GTF.

swan v1.0.2

Minor improvements

• Allows for exon entires to be in whatever order when loading a GTF

swan v1.0.1

Minor bug fixes and improvements for

• Added threading option in gen_report which will help Swan run better on clusters
• Patched a bug where edges can be exons and introns
• Patched a bug that remained in the code after internal testing for loading from a TALON db

swan v1.0

First public release!
Features include:

• Transcriptome loading via GTF or TALON database
• Transcript abundance support
• Transcriptome merging and tracking presence/absence of transcript models in each datasets
• Differential gene and transcript expression tests
• Detection of isoform switching genes
• Detection of novel exon skipping and intron retention events
• Unique visualization options to facilitate complexity of alternative splicing in datasets

swan 0.0.9

Added patch networkx command

swan 0.0.5

Patching pip setups