Ecosyste.ms: Issues

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GitHub / open2c/bioframe issues and pull requests

#120 - complement and subtract are very slow with large number of features

Issue - State: closed - Opened by agalitsyna over 2 years ago - 1 comment
Labels: enhancement

#119 - binnify with single chromosome

Issue - State: closed - Opened by Phlya over 2 years ago - 2 comments

#118 - is_contained for chromosome arms broken?

Issue - State: closed - Opened by Phlya over 2 years ago - 4 comments

#117 - factor out seq_gc from frac_gc

Pull Request - State: closed - Opened by gfudenberg over 2 years ago

#116 - bin-table operations

Issue - State: open - Opened by agalitsyna over 2 years ago - 1 comment
Labels: enhancement

#115 - fetch_centromeres without information of centromeres

Issue - State: closed - Opened by skytguuu over 2 years ago - 5 comments

#114 - make_viewframe takes forever on 100_000 entries

Issue - State: open - Opened by sergpolly over 2 years ago - 1 comment
Labels: enhancement

#113 - add-specs-update-readme

Pull Request - State: closed - Opened by gfudenberg over 2 years ago

#112 - Patch release for last 2 small fixes

Issue - State: closed - Opened by nvictus over 2 years ago - 1 comment

#111 - readme-and-small-tutorial-fix

Pull Request - State: closed - Opened by gfudenberg almost 3 years ago - 1 comment

#110 - guide-performance-updates

Pull Request - State: closed - Opened by gfudenberg almost 3 years ago - 2 comments

#109 - Guide update

Pull Request - State: closed - Opened by gfudenberg almost 3 years ago

#108 - Add cols_view to relevant ops

Pull Request - State: closed - Opened by Phlya almost 3 years ago - 1 comment

#107 - Local sources of truth for common genome assembly metadata

Issue - State: closed - Opened by nvictus almost 3 years ago
Labels: enhancement

#106 - Io cleanup

Pull Request - State: closed - Opened by gfudenberg almost 3 years ago - 1 comment

#105 - read_table behaviour with more names than columns

Issue - State: closed - Opened by Phlya almost 3 years ago - 3 comments

#104 - fix error in is_contained

Pull Request - State: closed - Opened by gfudenberg almost 3 years ago

#103 - motifs_per_peak calculated incorrectly in tutorial_assign_motifs_to_peaks.ipynb

Issue - State: closed - Opened by vbchavali about 3 years ago
Labels: bug

#102 - make_viewframe(clr.chromsizes) should use chromosomes as names, not UCSC

Issue - State: closed - Opened by sergpolly about 3 years ago - 1 comment
Labels: question

#101 - assign_view and other operations with view_df: cols argument applied to both df and view_df

Issue - State: closed - Opened by Phlya about 3 years ago - 3 comments
Labels: enhancement

#100 - Candidate bug report

Issue - State: closed - Opened by yanchunzhang about 3 years ago - 2 comments

#99 - jaspar url update

Pull Request - State: closed - Opened by gfudenberg about 3 years ago - 1 comment

#98 - Link In Tutorial Not Updating

Issue - State: closed - Opened by vbchavali about 3 years ago - 1 comment

#97 - should we add is_equal to checks for frames comparison (the way we want it) ?

Issue - State: open - Opened by sergpolly about 3 years ago - 1 comment
Labels: question

#96 - right now pysam dependency is failing with Python=3.9

Issue - State: closed - Opened by sergpolly about 3 years ago - 5 comments

#95 - make sure is_sorted works when df_view_col=None

Pull Request - State: closed - Opened by sergpolly about 3 years ago - 8 comments

#93 - More assemblies

Pull Request - State: closed - Opened by nvictus about 3 years ago

#92 - 0.5.0 roadmap

Issue - State: closed - Opened by gfudenberg over 3 years ago - 1 comment
Labels: enhancement

#91 - behavior of on=[]

Issue - State: open - Opened by gfudenberg over 3 years ago - 2 comments
Labels: enhancement

#90 - Add detailed assembly metadata

Pull Request - State: closed - Opened by nvictus over 3 years ago

#89 - dropping 3.6

Pull Request - State: closed - Opened by gfudenberg over 3 years ago

#88 - add error chaining for is_viewframe

Issue - State: open - Opened by gfudenberg over 3 years ago
Labels: enhancement

#86 - added natsort option to ops.sort_bedframe

Pull Request - State: closed - Opened by luisdiaz1997 over 3 years ago - 5 comments

#84 - fetch_centromeres error

Issue - State: closed - Opened by skytguuu over 3 years ago - 4 comments

#83 - delete-split-update-make_chromarms

Pull Request - State: closed - Opened by gfudenberg over 3 years ago - 13 comments

#82 - docstrings, guide, and suffixes=("","_")

Pull Request - State: closed - Opened by gfudenberg over 3 years ago - 1 comment

#81 - Organize imports

Pull Request - State: closed - Opened by nvictus over 3 years ago - 4 comments

#80 - from_* constructors behavior is inconsistent with the type of input - should not generate name-column by default

Issue - State: closed - Opened by golobor over 3 years ago - 4 comments
Labels: enhancement

#79 - doc-updates

Pull Request - State: closed - Opened by gfudenberg over 3 years ago - 1 comment

#78 - closest-subtract_now_groupby-observed=True

Pull Request - State: closed - Opened by gfudenberg over 3 years ago

#77 - verify_column_names_informative-error-for-repeated-columns

Pull Request - State: closed - Opened by gfudenberg over 3 years ago

#76 - merge-reset-index_issues-70

Pull Request - State: closed - Opened by gfudenberg over 3 years ago

#75 - fix-select-cols=alt_names

Pull Request - State: closed - Opened by gfudenberg over 3 years ago

#74 - bioframe select

Issue - State: closed - Opened by gfudenberg over 3 years ago - 1 comment

#73 - standardize functions to read various "bioframes" from file

Issue - State: closed - Opened by sergpolly over 3 years ago - 3 comments
Labels: enhancement, question

#72 - io.to_bed()

Issue - State: closed - Opened by golobor over 3 years ago - 2 comments
Labels: enhancement

#70 - merge "breaks combinatorially" when input DataFrame has duplicate indices

Issue - State: closed - Opened by sergpolly over 3 years ago - 1 comment
Labels: bug

#64 - should frac_gene be rename frac_RNA?

Issue - State: closed - Opened by gspracklin almost 4 years ago - 4 comments

#61 - uninformative errors for repeated column names

Issue - State: closed - Opened by gfudenberg almost 4 years ago
Labels: enhancement

#59 - in subtract(), add keep_order agrument

Issue - State: closed - Opened by golobor almost 4 years ago - 2 comments
Labels: enhancement

#56 - v0.2.0 updates

Pull Request - State: closed - Opened by nvictus almost 4 years ago

#48 - 0.3.0 roadmap

Issue - State: closed - Opened by golobor over 4 years ago - 6 comments

#46 - value types casting issues, pd.NA and pd.Categorical ....

Issue - State: closed - Opened by sergpolly over 4 years ago - 5 comments

#45 - bioframe.closest drops values if chromosome is missing in other

Issue - State: closed - Opened by mimakaev over 4 years ago - 3 comments

#43 - Creating a more extensive and generative test suite?

Issue - State: open - Opened by endrebak over 4 years ago
Labels: enhancement

#37 - Find a way to ensure alignment of two interval tables.

Issue - State: open - Opened by golobor over 4 years ago - 5 comments
Labels: enhancement

#36 - Make function coverage_track() to create base-pair resolution coverage tracks

Issue - State: open - Opened by golobor over 4 years ago - 1 comment
Labels: enhancement

#34 - EncodeClient, UCSCClient enhancements

Issue - State: open - Opened by gfudenberg over 4 years ago - 1 comment
Labels: enhancement

#26 - Operations on signal tracks

Issue - State: open - Opened by Phlya over 4 years ago - 1 comment
Labels: enhancement

#25 - 2D interval operations

Issue - State: open - Opened by Phlya over 4 years ago - 2 comments
Labels: enhancement

#18 - copy array operation functions from cooler.util to bioframe.arrops

Issue - State: closed - Opened by golobor over 4 years ago - 3 comments
Labels: question

#8 - provide a unified method to fetch centromeres

Issue - State: closed - Opened by golobor about 6 years ago - 5 comments

#4 - Add a function to make a binned table with gene density

Issue - State: closed - Opened by golobor almost 7 years ago - 5 comments