biocore/calour issues and pull requests

#303 - join_experiments() raises as pandas future warning

Issue - State: open - Opened by amnona 27 days ago
Labels: bug

#302 - mRNA experiment support

Pull Request - State: closed - Opened by amnona about 1 month ago - 2 comments

#301 - add documentation for new functions/modules

Issue - State: open - Opened by amnona about 1 month ago
Labels: enhancement

#300 - Add permanova support

Issue - State: open - Opened by amnona about 1 month ago
Labels: enhancement

#299 - command history for save and load

Issue - State: open - Opened by amnona about 1 month ago
Labels: enhancement

#298 - Bugfix diff abundance

Pull Request - State: closed - Opened by amnona about 2 months ago - 2 comments

#297 - Diff abundance bug fix

Pull Request - State: closed - Opened by amnona about 2 months ago

#296 - Update INSTALL.md

Pull Request - State: closed - Opened by amnona 2 months ago

#295 - Mpl37fix (#63)

Pull Request - State: closed - Opened by amnona 2 months ago - 1 comment

#294 - No documentation for new version?

Issue - State: open - Opened by DrJStrudwick 3 months ago

#293 - New versions not on pypi?

Issue - State: open - Opened by DrJStrudwick 3 months ago

#292 - update installation instructions

Issue - State: closed - Opened by amnona 3 months ago - 1 comment
Labels: bug

#291 - working with small/negative values

Issue - State: open - Opened by amnona 3 months ago
Labels: bug

#290 - filter_samples does not work with numpy array for value

Issue - State: open - Opened by amnona 3 months ago
Labels: bug

#289 - Mpl37fix

Pull Request - State: closed - Opened by amnona 5 months ago

#288 - use pandas data frame as metadata input

Issue - State: open - Opened by baobabprince 10 months ago

#287 - Struggling to Figure Out The Structure of Biom File

Issue - State: closed - Opened by hlee885 11 months ago - 1 comment

#286 - Mpl37 plot fix and additional type hints for methods

Pull Request - State: closed - Opened by amnona about 1 year ago

#285 - add option to drop if exists the new column in join_metadata_fields()

Issue - State: open - Opened by amnona over 1 year ago
Labels: enhancement

#284 - when doing cluster_features for metaphlan output (shotgun metagenomics), need to set different presence threshold

Issue - State: open - Opened by amnona over 1 year ago

#283 - filter_samples does not work when supplying values as a numpy array

Issue - State: open - Opened by amnona over 1 year ago
Labels: bug

#282 - missing documentation in the calour .io docs for to/from pandas

Issue - State: open - Opened by amnona over 1 year ago
Labels: enhancement

#281 - add type hints

Pull Request - State: closed - Opened by amnona almost 2 years ago

#280 - enable sep=XX parameter in _read_metadata()

Pull Request - State: closed - Opened by amnona almost 2 years ago - 1 comment

#279 - Update reporting to diff abundance and filtering

Pull Request - State: closed - Opened by amnona almost 2 years ago - 1 comment

#278 - Better diff_abundance_enrichment() plot

Pull Request - State: closed - Opened by amnona almost 2 years ago - 1 comment

#277 - add info after loading an experiment

Pull Request - State: closed - Opened by amnona almost 2 years ago - 4 comments

#276 - remove normaliztion check warning from filter_by_data()

Pull Request - State: closed - Opened by amnona almost 2 years ago - 4 comments

#275 - fix _read_metadata() to show as warning/info only the summary

Pull Request - State: closed - Opened by amnona almost 2 years ago - 1 comment

#274 - fix heatmap() inplace colormap modification depracation warning

Pull Request - State: closed - Opened by amnona almost 2 years ago - 4 comments

#273 - Bugfixes for manipulation.py

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

#272 - fix join_metadata() and version bump

Pull Request - State: closed - Opened by amnona almost 2 years ago - 1 comment

#271 - get warning when doing "read_amplicon()"

Issue - State: closed - Opened by amnona almost 2 years ago
Labels: bug

#270 - set default (white) for missing colors in barx_colors in plot()

Issue - State: open - Opened by amnona about 2 years ago

#269 - enable rotation for barx_label_kwargs in plot()

Issue - State: open - Opened by amnona about 2 years ago

#268 - raise appropriate error when plotting an empty experiment

Issue - State: open - Opened by amnona about 2 years ago

#267 - Installation problems

Issue - State: open - Opened by baobabprince about 2 years ago

#266 - report number of samples and features after read()

Issue - State: closed - Opened by amnona over 2 years ago

#265 - Problem with rarifying unnormalized experiments

Issue - State: open - Opened by amnona over 2 years ago
Labels: bug

#264 - raise warning if value does not exist in diff_abundance

Issue - State: open - Opened by amnona over 2 years ago

#263 - join_experiments() cannot work if experiment field already exists

Issue - State: closed - Opened by amnona over 2 years ago

#262 - filter_prevalence() field parameter not working

Issue - State: open - Opened by amnona over 2 years ago
Labels: bug

#261 - enable single value input in filter_by_metadata()

Issue - State: open - Opened by amnona over 2 years ago

#260 - join_experiments need to set md5 data in the exp info

Issue - State: closed - Opened by amnona over 2 years ago

#259 - norm() for heatmap - maybe supply also a string option for "linear" or "log"

Issue - State: open - Opened by amnona almost 3 years ago
Labels: enhancement

#258 - io.read() has the sep='\t' set so cannot re-set it in the sample_metadata_kwargs

Issue - State: open - Opened by amnona almost 3 years ago
Labels: bug

#257 - warning for changing colormap for heatmap when doing plot()

Issue - State: closed - Opened by amnona almost 3 years ago
Labels: bug

#256 - feat: support https on the exported heatmap

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

#255 - Fix sample_in_row for read_ms

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

#254 - fix dbbact-calour version testing

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

#253 - testing for travis - do not merge

Pull Request - State: open - Opened by amnona about 3 years ago

#252 - Dbbact version

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

#251 - export_heatmap enable different field for taxonomy and heatmap y-axis

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

#250 - Db fix

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

#249 - feat(export_html.py): update heatmap low color to black and remove **kwargs

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

#248 - make html export use https for obtaining dsj3

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

#247 - please ignore - testing

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

#246 - please ignore - Test travis

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

#245 - Byebye skbio

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

#244 - fix bug when not using all samples in paired test

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

#243 - first and last feature in heatmap

Issue - State: open - Opened by amnona over 3 years ago

#242 - normalize diff_abundance results with rank to -1/1

Issue - State: open - Opened by amnona over 3 years ago

#241 - Paired groups

Pull Request - State: closed - Opened by amnona over 3 years ago - 2 comments

#240 - fix bar_label_kwargs so rotation works

Pull Request - State: open - Opened by amnona over 3 years ago - 4 comments

#239 - fix bug:"numpy.ndarray" object has no attribute "median"

Pull Request - State: closed - Opened by maque4004 over 3 years ago

#238 - add cmd+click to selection

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

#237 - add 'cmd' in addition to 'super' for heatmap multiple selection

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

#236 - summarize warning if lots of samples not found in read()

Issue - State: closed - Opened by amnona over 3 years ago
Labels: enhancement

#235 - Paired testing for diff. abundance

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

#234 - Add an option to read metadata from csv files

Issue - State: open - Opened by baobabprince over 3 years ago

#233 - inplace in join_metadata_fields is True by default

Issue - State: closed - Opened by amnona over 3 years ago
Labels: bug

#232 - filter_mean_abundance on unnormalized data

Issue - State: open - Opened by amnona almost 4 years ago
Labels: bug

#231 - bug in join_metadata_fields

Issue - State: closed - Opened by amnona almost 4 years ago
Labels: bug

#230 - fix debug message in delete sequence from annotation

Pull Request - State: closed - Opened by amnona almost 4 years ago - 1 comment

#229 - problem with plot normalization for non ampliconexperiment

Issue - State: open - Opened by amnona almost 4 years ago

#228 - add value to Experiment.iterate()

Pull Request - State: closed - Opened by amnona almost 4 years ago - 1 comment

#227 - Delete a line of duplicate content

Pull Request - State: closed - Opened by SJ-Wang-tech almost 4 years ago - 2 comments

#226 - Correct the error

Pull Request - State: closed - Opened by SJ-Wang-tech almost 4 years ago

#225 - add values to experiment.iterate

Issue - State: closed - Opened by amnona almost 4 years ago - 1 comment
Labels: enhancement

#224 - update version

Issue - State: closed - Opened by amnona almost 4 years ago

#223 - add per row normalization to heatmap

Issue - State: open - Opened by amnona almost 4 years ago
Labels: enhancement

#222 - move reorder() to avoid `axis` function argument not converted and avoid its running not recorded

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

#221 - add random_seed to permute_data

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

#220 - fix cluster_features() bug

Pull Request - State: closed - Opened by RNAer almost 4 years ago - 1 comment

#219 - Ratio experiment

Pull Request - State: closed - Opened by amnona almost 4 years ago - 2 comments

#218 - add Experiment.iterate()

Pull Request - State: closed - Opened by amnona almost 4 years ago - 1 comment

#217 - Experiment.reorder() is not getting the axis correctly

Issue - State: closed - Opened by amnona almost 4 years ago - 1 comment
Labels: bug

#216 - cluster_features broken

Issue - State: closed - Opened by amnona almost 4 years ago
Labels: bug

#215 - Heatmap nan

Pull Request - State: closed - Opened by amnona almost 4 years ago - 2 comments

#214 - make skbio dependance optional

Pull Request - State: closed - Opened by amnona almost 4 years ago - 1 comment

#213 - Ms1 experiment

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

#212 - get rid of skbio

Issue - State: open - Opened by amnona almost 4 years ago
Labels: enhancement

#211 - change random_seed to random_state

Pull Request - State: closed - Opened by amnona almost 4 years ago - 3 comments

#210 - fix mannwhitney warning

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

#209 - Dbbact metadata

Pull Request - State: closed - Opened by amnona almost 4 years ago - 1 comment

#208 - update changelog

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

#207 - Add unique values iterator over samples

Issue - State: closed - Opened by amnona almost 4 years ago - 1 comment
Labels: enhancement

#206 - add un-normalize to save()

Issue - State: open - Opened by amnona almost 4 years ago
Labels: enhancement

#205 - create ratioexperiment class

Issue - State: open - Opened by amnona almost 4 years ago
Labels: enhancement

#204 - move qt5 term enrichment gui to database modules

Pull Request - State: closed - Opened by amnona about 4 years ago

GitHub / biocore/calour issues and pull requests