open2c/bioframe

Issues

• Bioframe.overlap RAM error

  #219 opened 5 months ago by talipzengin
  1

• Two tests segfault on s390x

  #215 opened 6 months ago by penguinpee
  3

• Typo in the changelog

  #214 opened 6 months ago by penguinpee
  0

• Merging based on unrelated intervals possible?

  #212 opened 6 months ago by marade
  0

• Python 3.13: test_assembly_info fails with AttributeError

  #209 opened 7 months ago by penguinpee
  2

• feature request

  #208 opened 8 months ago by WANGchuang715
  1

• Bring back GTF attributes parser?

  #141 opened 2 years ago by nvictus
  2

• Restore and document additional `return_input` args for `overlap`

  #197 opened 8 months ago by nvictus
  0

• Strand-aware expand (bedtools slop)

  #144 opened 2 years ago by ivirshup
  13

• complement and subtract are very slow with large number of features

  #120 opened 9 months ago by agalitsyna
  1

• make_viewframe takes forever on 100_000 entries

  #114 opened 3 years ago by sergpolly
  1

• default dtypes & core.construction

  #188 opened 10 months ago by smitkadvani
  4

• overlap between a point and a segment is broken

  #183 opened 9 months ago by golobor
  0

• bioframe.assign_view drop_unassigned drops all NaNs?

  #160 opened 2 years ago by Phlya
  3

• test_make_chromarms fails with TypeError using NumPy 1.24.4

  #189 opened 9 months ago by penguinpee
  2

• CI: Implement Issue Template for bioframe Repository

  #190 opened 10 months ago by milandvijay
  0

• Change in goldenpath URL

  #186 opened a year ago by nvictus
  1

• to_bigwig: wrong format for chromsizes

  #168 opened a year ago by rusch-emma
  2

• subtract error in windows

  #169 opened a year ago by meisproject
  1

• non-standard column names in checks.is_contained

  #126 opened a year ago by Phlya
  1

• coverage crashes when `cols` is specified

  #173 opened a year ago by benjaminbauer
  2

• Streamlining input validation for ops

  #140 opened 2 years ago by nvictus
  0

• Passing metadata (/configuration?) through DataFrame.attrs

  #151 opened 2 years ago by ivirshup
  0

• reading bigwigs into dataframes

  #153 opened 2 years ago by gfudenberg
  0

• Assorted bugs and possibly undefined behavior in closest

  #167 opened a year ago by endrebak
  0

• Suggestion for updating the closest function.

  #163 opened 2 years ago by WANGchuang715
  6

• Deprecation of `is_categorical_dtype` in pandas 2

  #174 opened a year ago by benjaminbauer
  1

• make chromarms - broken, or changed?

  #175 opened a year ago by Phlya
  3

• Alternative DataFrame class(es) for OOC + speed

  #137 opened 2 years ago by ivirshup
  4

• Readthedocs error for closest(... direction_col='strand')

  #138 opened 2 years ago by ermakova
  4

• docs rendering issues

  #143 opened 2 years ago by gfudenberg
  2

• plot_intervals gives "ValueError: zero-size array to reduction operation maximum which has no identity" exception

  #135 opened 2 years ago by gokceneraslan
  3

• Move extract_centromeres to extras

  #142 opened 2 years ago by nvictus
  2

• select recently changed behavior causing issues in cooltools

  #145 opened 2 years ago by sergpolly
  0

• Local sources of truth for common genome assembly metadata

  #107 opened 2 years ago by nvictus
  0

• bin-table operations

  #116 opened 3 years ago by agalitsyna
  1

• strand-aware closest

  #129 opened 2 years ago by gfudenberg
  1

• Overlapping intervals in single bed

  #134 opened 2 years ago by krukanna
  2

• Allow start==stop for point data

  #127 opened 2 years ago by ivirshup
  5

• Feature idea: select_index – select that only returns indices

  #128 opened 2 years ago by ivirshup
  7

• updates for schemas

  #123 opened 2 years ago by gfudenberg
  8

• Option to change bedgraphToBigwig path

  #124 opened 2 years ago by agalitsyna
  0

• improve documentation for overlap "return_overlap" argument

  #122 opened 2 years ago by gonzalobenegas
  3

• is_contained for chromosome arms broken?

  #118 opened 2 years ago by Phlya
  4

• binnify with single chromosome

  #119 opened 2 years ago by Phlya
  2

• fetch_centromeres without information of centromeres

  #115 opened 3 years ago by skytguuu
  5

• Patch release for last 2 small fixes

  #112 opened 3 years ago by nvictus
  1

• motifs_per_peak calculated incorrectly in tutorial_assign_motifs_to_peaks.ipynb

  #103 opened 3 years ago by vbchavali
  0

• make_viewframe(clr.chromsizes) should use chromosomes as names, not UCSC

  #102 opened 3 years ago by sergpolly
  1

• read_table behaviour with more names than columns

  #105 opened 3 years ago by Phlya
  3