abagen - 0.1.4

- Python
Published by rmarkello over 4 years ago

abagen - 0.1.3

0.1.3 (June 18, 2021)

More bug fixes for (identified thanks to @richardajdear and @Silflame!) as well as some minor QOL updates for getting sample-level information from workflows.

• [REF] Handle atlases w/decimal vox sizes (#197), @rmarkello
• [REF] Re-orient img in leftify_atlas() (#193), @rmarkello
• [FIX] Fixes logger error w/reports (#192), @rmarkello
• [FIX] Error with donor-specific atlases and tolerance=0 (#191), @rmarkello
• [REF] Fix coordinates of getsamplesin_mask (#189), @rmarkello

- Python
Published by rmarkello over 4 years ago

abagen - 0.1.1

0.1.1 (March 29, 2021)

Small bug fix for when probe_selection='average' and a minor QOL update to check_atlas().

• [ENH] Add geometry/space option to check_atlas (#186), @rmarkello
• [FIX] Fixes 'average' probe selection bug (#185), @rmarkello

- Python
Published by rmarkello almost 5 years ago

abagen - 0.1

0.1 (March 25, 2021)

First minor release! :tada: This update brings some major changes to the codebase, including a massive internal refactoring to allow handling of surface parcellations, new methods for interpolating missing data, and more!

Important: as this is our first official minor release, note that the changes in this release are not backwards compatible with previous versions.

• [ENH] Adds interareal similarity thresholding (#184), @rmarkello
• [REF] Allow negative tolerance for surfaces (#183), @rmarkello
• [REF] Updates reports for missing param (#182), @rmarkello
• [DOC] Updates master refs to main (#181), @rmarkello
• [ENH] Adds interpolation options for missing data (#180), @rmarkello
• [REF] Updates mouse data cache location (#179), @rmarkello
• [FIX] Bugfix for lr_mirror parameter (#178), @rmarkello
• [ENH] Adds reporting of processing methods (#177), @rmarkello
• [FIX] Nan hemisphere designation (#176), @rmarkello
• [FIX] Addresses bug when tolerance=0 (#175), @rmarkello
• [TEST] Add py3.8 to azure tests (#174), @rmarkello
• [REF] Constrains centroid matching by atlas_info (#173), @rmarkello
• [REF] Updates CLI to match main workflow (#172), @rmarkello
• [REF] Modifies lr_mirror to accept single hemisphere mirroring (#171), @rmarkello
• [ENH] Add norm_structures parameter (#170), @rmarkello
• [ENH] Adds ability to handle surface parcellations (#169), @rmarkello
• [TEST] Parametrize test_resid_dist (#164), @4lovi4

- Python
Published by rmarkello almost 5 years ago

abagen - 0.0.8

0.0.8 (January 29, 2021)

Largely internal codebase changes, but an important bug fix for compatibility with newer versions of pandas.

Huge thanks to @4lovi4 for all their contributions!

• [FIX] Read_csv error when using pandas >= 1.2.0 (#167), @rmarkello
• [TEST] Change Azure VM image to fix SSL (#165), @rmarkello
• Adds Python 3.8 testing support to CircleCI (#163), @4lovi4
• issue #73 unquote url (#162), @4lovi4
• issue #80 doc string fix (#161), @4lovi4
• issue #139 readme fix (#160), @4lovi4

- Python
Published by rmarkello about 5 years ago

abagen - 0.0.7

0.0.7 (October 15, 2020)

Only two changes—but relatively impactful ones—including the addition of a new workflow-style function (abagen.get_samples_in_mask()) to get preprocessed tissue samples without aggregating in specific brain regions and the ability to provide parcellations in donor-native space (rather than MNI space).

Documentation has been updated to reflect all new features!

• [ENH] Adds handling for donor-specific atlases (#156), @rmarkello
• [ENH] Allows users to get microarray samples in mask (#155), @rmarkello

- Python
Published by rmarkello over 5 years ago

abagen - 0.0.5

0.0.5 (March 24, 2020)

This release includes quite a bit of new functionality, including:

• Several new gene/sample normalization methods,
• A fetcher / new loader functions for RNAseq data (abagen.fetch_rnaseq()),
• The ability to use RNAseq data for selecting probes (probe_selection='rnaseq), and
• A new donor_probes parameter for abagen.get_expression_data() to control how probe selection is performed

Check out the documentation for more details!

• [ENH] Adds new mechanisms for probe selection (#145), @rmarkello
• [ENH,REF] Adds RNAseq probe selection method (#144), @rmarkello
• [TEST] Fix Azure maybe? (#143), @rmarkello
• [ENH] Adds FreeSurfer data fetcher (#142), @rmarkello
• [ENH] Adds fetchers / loaders for RNAseq data (#140), @rmarkello
• [TEST] Adds Windows testing with Azure (#141), @rmarkello
• [FIX,ENH] Error in getexpressiondata, gene stability calculation (#136), @rmarkello
• [ENH,REF] New norms, utils, renamed modules (#135), @rmarkello

- Python
Published by rmarkello almost 6 years ago

abagen - 0.0.4

0.0.4 (February 26, 2020)

A new release with a small bugfix (#134) and a small fix-fix (#133)!

• [FIX] Coerce atlas dataobj to arr before indexing (#134), @rmarkello
• [REF] Drop probes with invalid/missing Entrez ID (#133), @rmarkello

- Python
Published by rmarkello about 6 years ago

abagen - 0.0.3

0.0.3 (November 26, 2019)

A new release with some added features but primarily a good bit of re-arranging in the primary abagen.get_expression_data() workflow. Notable changes include:

• New parameters region_agg, agg_metric, sample_norm, and gene_norm (the latter of which supplants donor_norm), controlling how microarray samples are normalized and aggregated across donors;
• Large reductions in memory usage (#130), such that the primary workflow should only use ~2GB of RAM at its peak; and,
• Migration to CircleCI for all testing purposes!

Special thanks to Vincent Bazinet (@VinceBaz), Ellen Wang (@Ellen8780), Romke Hannema (@rhannema), and Anthony Gifuni (@gifuni) for their contributions!

• [REF] Adds option to suppress norm warnings (#132), @rmarkello
• [ENH,REF] Adds new region_agg parameter (#131), @rmarkello
• [REF] Massive reduction in memory usage (#130), @rmarkello
• [FIX] Solves pandas bug with max_variance method (#128), @gifuni
• [STY] Fixes trailing whitespace (#129), @rmarkello
• [FIX] Fixes strange TypeError for pc_loading (#1), @rmarkello
• [REF] Ensures integer DataFrame when return_count=True (#127), @rhannema
• [ENH] Add fetcher for donor info (#126), @Ellen8780
• [REF,ENH] Modifies and adds normalization procedures (#119), @rmarkello
• [TEST] Updating CircleCI build (#122), @rmarkello
• [TEST] TravisCI --> CircleCI (#121), @rmarkello
• [REF] Removes .get_data() nibabel calls (#120), @rmarkello
• [FIX] Specify engine='python' in pandas queries (#117), @VinceBaz

- Python
Published by rmarkello over 6 years ago

abagen - 0.0.2

0.0.2 (September 19, 2019)

This release comes with a lot of new changes, including:

• Several new arguments for abagen.get_expression_data(), including new probe selection methods, donor normalization techniques, and hemispheric mirroring of tissue samples;
• A command-line version of the primary workflow accessible via the abagen command;
• Improved data handling, using $HOME/abagen-data as the default storage location for data from the AHBA;
• New functionality for fetching raw AHBA donor MRI scans;
• Zenodo integration to make it easy to cite abagen; and,
• Massive documentation overhauls, with a dramatically updated user guide and API reference!

Special thanks to Golia Shafiei (@gshafiei), Ying-Qiu Zheng (@yingqiuz), James Frierson (@JamesFrierson1), and Arda Kosar (@abkosar) for their contributions.

• [MNT] Finishes Zenodo integration (#109), @rmarkello
• [MNT] Adds framework for Zenodo integration (#108), @rmarkello
• [REF] Fixes one-donor bug in getexpressiondata() (#107), @rmarkello
• [REF] Identifies hippocampus as subcortex in Allen ontology (#106), @rmarkello
• [DOC] Updates documentation + contributing (#105), @rmarkello
• [REF] Mirroring before probe filtering (#101), @rmarkello
• [FIX] Installation not correctly bundling package data (#102), @rmarkello
• [MNT] Docs / package structure updates in prep for 0.2.0 (#95), @rmarkello
• [REF] abagen.io functions don't copy dataframes by default (#94), @rmarkello
• [FIX] Fixes broken include directive in API reference (#91), @rmarkello
• [ENH] Adds parameter for normalizing donor microarray expression values (#90), @rmarkello
• [ENH] Adds option to mirror samples across L/R hemispheres (#87), @rmarkello
• [ENH] Adds CLI for abagen.get_expression_data functionality (#82), @rmarkello
• [ENH] Adds ability to fetch raw AHBA MRIs (#85), @rmarkello
• [ENH] Adds ability to query gene groups (#83), @rmarkello
• [MNT,REF] Updates install, versioning, dependencies (#84), @rmarkello
• [REF] Adds brainstem to abagen.process ontology (#81), @rmarkello
• [DOC] Updates API documentation (#76), @rmarkello
• [REF,ENH] Adds new abagen.probes module (#67), @rmarkello
• [REF] Changes data directory locator for abagen data (#66), @rmarkello
• [FIX] Fixes doctest in abagen.mouse (#65), @rmarkello
• [REF] Removes .get_values() references (#64), @rmarkello
• [DOC] Adds logging to workflow functions (#61), @rmarkello
• Fixed abagen.mouse column ordering (#62), @abkosar
• [DOC] Update refs and http (#60), @rmarkello
• [REF] Use cached alleninf coordinates only (#59), @rmarkello
• [FIX] Removes RuntimeWarning in example code (#58), @rmarkello
• Updated README to include Allen Institute citations and disclaimers (#57), @JamesFrierson1
• [FIX] Catches AttributeError w/pandas fastparquet (#41), @rmarkello
• [REF] Updates getexpressiondata() (#38), @rmarkello
• [TEST] Fixes tests (#34), @rmarkello
• Add mouse features (#32), @yingqiuz
• [TEST] Fix pytest version and update travis (#33), @rmarkello
• [TEST] Update travis testing (#31), @rmarkello
• [FIX] More fixes for atlas numbering (#30), @rmarkello
• [FIX] Allow non-sequential atlas numbering (#29), @rmarkello
• [ENH] Adds input check for remove_distance() (#28), @rmarkello
• [ENH] Allow label exclusion in remove_distance() (#27), @rmarkello
• [REF] Changes remove_distance() inputs (#26), @rmarkello
• [ENH] Add function for aggregating donors (#25), @rmarkello
• [ENH] Adds reannotated probe information (#24), @rmarkello
• [ENH] Adds abagen.correct for postprocessing (#20), @rmarkello
• [TEST] Removes pytest capturing (#23), @rmarkello
• [TEST] Calculates coverage only for extras (#22), @rmarkello
• [DOC] Updates doc-strings for primary functions (#19), @rmarkello
• [TEST] Add early test to reduce timeouts (#21), @rmarkello
• [FIX] Adds updated MNI coordinates file as backup (#17), @rmarkello
• [DOC] Updates default tolerance (#16), @gshafiei

- Python
Published by rmarkello over 6 years ago

abagen - 0.0.2-rc.1

- Python
Published by rmarkello over 6 years ago

abagen - 0.0.1

Initial release of abagen, a toolbox for working with the Allen Brain Atlas human genetics data.

- Python
Published by rmarkello over 7 years ago