Release v0.5.1

[0.5.1] - 2023-12-19

Fixed

• ANANSE influence (with whitelists) AttributeError: 'numpy.ndarray' object has no attribute 'index'
• ANANSE plot ValueError: Unable to determine Axes to steal space for Colorbar.
• ANANSE network pandas.iloc[] deprecationWarning

Release v0.5.0

[0.5.0] - 2023-10-15

Added

• ananse influence now accepts a whitelist of genes and/or interactions from the network
  • these will be added back into the influence network after selecting top edges.

Fixed

• No region overlap (pandas str.replace() no longer uses regex by default)
• Error while merging duplicate genes in ANANSE binding

Release v0.4.1

[0.4.1] - 2023-01-12

Added

• anane view can now return factory activity with --activity
• anane view also accepts -n for all sub-option (list TFs, list regions and activity)

Changed

• ananse network uses slightly less memory, and should now keep going unless all memory is used.

Fixed

• ananse influence now throws a descriptive error if source and target networks are identical
• ananse influence now uses scipy >=1.9, which fixes an error in mannwhitneyu(method="auto")
• uploaded correct non-human CAGE-seq models

Release v0.4.0

[0.4.0] - 2022-06-02

Added

• CAGE-seq support!
  • for more details, check out https://github.com/vanheeringen-lab/ANANSE-CAGE
• ananse.binding can now optionally accept a raw counts file instead of BAM files.
  • ananse.binding now has a (case-insensitive) --columns argument to filter the counts table by.
• ananse.view now optionally accepts regions and tfs, to filter the output.
• ananse.view can also output the header of (up to) n TFs & regions.
• ananse.view can also output a list of all regions or tfs.
• ananse network will check the gene name overlap between the expression files, the motif2factor.txt and the tfs (#120).
  • if overlap is low, and a genomepy genome/annotation is given, the symbols are converted to gene names, similar to gimme motif2factors
  • if overlap is none, an informative error is raised
• ananse network can now accept one or more column names to use from the expression file (e.g. column names from a counts table)
• ananse network now optionally accepts regions and tfs, to filter the binding.h5 content.
• ananse network can (at least internally) output an expression network, binding network or expression-binding network.
• ananse influence will also check the gene overlap (between the merged networks and the DEgenes) (#120).
  • if overlap is low, and a genomepy genome/annotation is given, the symbols are converted to gene names, similar to gimme motif2factors
  • if overlap is none, an informative error is raised
• ananse plot now optionally accepts a file type for the output plots (e.g. pdf, png)
• all ananse CLI functions now have a default output file/dir
• ADDITIONAL UNIT TESTS!
• TEST DATA! See tests/data/GRCz11_chr9
  • including a README.md on the creation and bash command for every function.

Changed

• Now uses em-dash as gene separator (—), instead of underscore (_). Should solve issues with gene names having underscores, as em-dash is a pretty obscure char.
• ananse binding will ignore BLACKLIST_TFS in motif2factors.txt. Currently, this is only the artifact "NO ORTHOLOGS FOUND".
• refactored jaccard stuff
  • reduced jaccard graph size (no more duplicates/self edged)
  • reduced logger messages (max 1 message per motif now)
• ananse binding documentation changed to clearly reflect the complexity of non-hg38
  • with expandable sections to reduce clutter for the hg38 gang
• ananse binding will now only scan the motifs in the analysis
• ananse binding will now only scan the regions overlapping the pfmscorefile and regions (if both are given)
• changed the hardcoded .txt file extensions in ananse plot to .tsv
• ananse network now loads the gene bed into pyranges once (instead of once per chromosome).
• ananse influence now uses the top 500.000 TF-gene interactions. By default, filtering for highest positive interactions.
• cleaned up ananse --help messages

Removed

• ananse binding now requires a genome fasta (to create _factor_activity)
• legacy code (enhancer_binding is now bed, containing only the relevant code)

Fixed

• jaccard index with custom pfmfiles
• ananse view --help
• issue in ananse binding when specified regions have no bam coverage (#153)
• issue in ananse binding when probability cant be found for any TF (#147)
• issue in ananse network when executing run_network() from python
• ananse network merges duplicate genes and transcription factors (#142)
• issue in ananse influence when using only 1 network
• ananse influence made slightly much faster.
• ananse influence hopefully uses less memory now.
• ananse influence now skips pvalues for TFs without any targets or non-targets.
• ananse plot will no longer warn you incorrectly about your "weight"
• ananse plot error "OSError: Format: "dot" not recognized."

Version 0.3.0

[0.3.0] - 2021-07-14

Added

• ananse view command to view the binding.h5 file that is now produced by ananse binding.
• Support for region /table file as input to ananse binding.
• In-built support for mouse.
• Warning with information if another species than human or mouse is used.
• Warning if annotation files don't match for ananse influence.
• Improved logging messages.
• Better checking of input files.

Changed

• ananse binding produces a HDF5 file (binding.h5) which is much smaller on disk.
• Better memory performance of ananse network.
• Removed threshold for differential network in ananse influence.

Fixed

• Gene names don't get capitalized in ananse influence (#87).

Version 0.2.2

Bugfix release

• Multiple expression files allowed for ananse network.
• Fix error relating to fin_epxression in ananse influence.

Version 0.2.1

Bugfix release.

• Add -o, --outfile argument to ananse network
• Include benchmark code

Version v0.2.0

ANANSE release v0.2.0.

Changes:

• Complete redesign of command line interface.
• More advanced model transcription factor binding prediction.
• Incorporate transcription factor activity in network inference.
• Can use H3K27ac and/or ATAC-seq data.

Version 0.1.7

• Fix “ImportError: dlopen: cannot load any more object with static TLS”

ANANSE-Release v0.1.6

Change input degene file. The log2FoldChange should be a positive number if this gene is up regulated, and negative number if this gene is down regulated.