Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / jbloomlab/dms_variants issues and pull requests

#88 - add outer flank regions for `IlluminaBarcodeParser`

Pull Request - State: closed - Opened by jbloom 8 months ago

#87 - update to use newer versions of dependencies

Pull Request - State: closed - Opened by jbloom 10 months ago

#86 - scipy.flip() is deprecated

Issue - State: closed - Opened by ckikawa 10 months ago

#85 - deprecation warning

Issue - State: open - Opened by jbloom over 1 year ago - 4 comments

#84 - add `primary_target_only` to `prob_escape` (becomes version 1.4.3)

Pull Request - State: closed - Opened by jbloom over 1 year ago

#83 - fix failures of `flake8` and tests due to changed versions

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

#82 - Checks failing on pull request

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

#81 - adds ftol as option to fit_models

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

#80 - Optionally enforce zero observed phenotype for WT in global epistasis model

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

#79 - fix doc typo

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

#78 - prob_escape example typo

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

#77 - add `prob_escape` (version 1.4)

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

#76 - `black` format code and test on Travis

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

#75 - in-frame deletions as a valid character

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

#74 - added `inverse_simpson_index (v 1.2.0)

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

#73 - Errors while installing dms_variants 1.1.0 with python 3.8

Issue - State: closed - Opened by yeli7068 almost 3 years ago - 3 comments

#72 - pip install issue

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

#71 - added `allowed_aa_muts` to `simulate_CodonVariantTable`

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

#70 - version 1.0

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

#69 - fix plotting bugs

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

#67 - Barcodes must match case found in sequencing files to be counted

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

#66 - fix bug in `extra_cols` for `from_variant_count_df`

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

#65 - extra_cols in

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

#64 - add `extra_cols` to `CodonVariantTable.from_variant_count_df`

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

#63 - fix version, it is 0.8.7

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

#62 - Fix rarefy bcs

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

#61 - rarefyBarcodes maxpoints dtype incompatibility

Issue - State: closed - Opened by khdcrawford over 3 years ago - 2 comments

#60 - remove some unlikely use cases from tests / docs

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

#59 - fix compile args for windows

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

#57 - added `dms_variants.pdb_utils.reassign_b_factor`

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

#56 - classify aa muts as single nt accessible (v0.8.4)

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

#55 - unpin `plotnine`

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

#54 - fix bug in `filter_by_subs_observed` (v 0.8.2)

Pull Request - State: closed - Opened by jbloom over 4 years ago

#53 - Added `filter_by_subs_observed` function

Pull Request - State: closed - Opened by jbloom over 4 years ago

#52 - add `escape_scores` score type `frac_escape` (v 0.8.1)

Pull Request - State: closed - Opened by jbloom over 4 years ago

#51 - fix typo in `BinaryMap` docs

Pull Request - State: closed - Opened by jbloom over 4 years ago

#50 - version 0.8.0: update / fix `CodonVariantTable.escape_score`

Pull Request - State: closed - Opened by jbloom over 4 years ago

#49 - Allow `classifyVariants` to take scores by `aa_substitutions`

Issue - State: closed - Opened by ajgreaney over 4 years ago - 1 comment

#48 - Fix `CodonVariantTable.escape_scores` bug that gives null escape scores

Pull Request - State: closed - Opened by jbloom over 4 years ago

#47 - version 0.7.0

Pull Request - State: closed - Opened by jbloom over 4 years ago

#46 - stop pinning `plotnine` to 0.6.0

Pull Request - State: closed - Opened by jbloom over 4 years ago

#45 - fix bug in `CodonVariantTable.classifyVariants` w multiple targets

Pull Request - State: closed - Opened by jbloom over 4 years ago

#44 - `add_frac_counts` & `plotCountsPerVariant` added to `CodonVariantTable`

Pull Request - State: closed - Opened by jbloom over 4 years ago

#43 - `CodonVariantTable.classifyVariants` handles non-primary targets

Pull Request - State: closed - Opened by jbloom over 4 years ago

#42 - `classifyVariants` handles non-primary targets

Pull Request - State: closed - Opened by jbloom over 4 years ago

#41 - add `CodonVariantTable.escape_scores`

Pull Request - State: closed - Opened by jbloom over 4 years ago

#40 - speed up `classifyVariants`

Pull Request - State: closed - Opened by jbloom over 4 years ago

#39 - version 0.6: `CodonVariantTable` handles secondary targets

Pull Request - State: closed - Opened by jbloom over 4 years ago

#38 - `plotCumultMutCoverage` y-axis extends from 0 to 1

Pull Request - State: closed - Opened by jbloom over 4 years ago

#37 - `CodonVariantTable` plots no facet title if 1 lib

Pull Request - State: closed - Opened by jbloom over 4 years ago

#36 - print bottleneck estimates in `estimateBottleneck` docs

Pull Request - State: closed - Opened by jbloom almost 5 years ago

#35 - version 0.5.0 (bottleneck likelihood, multiple latent phenotypes)

Pull Request - State: closed - Opened by jbloom almost 5 years ago

#34 - estimate pre- to post-selection bottlenecks

Pull Request - State: closed - Opened by jbloom almost 5 years ago

#33 - bottleneck likelihood for global epistasis models

Pull Request - State: closed - Opened by jbloom almost 5 years ago

#32 - multiple latent phenotypes in global epistasis models

Pull Request - State: closed - Opened by jbloom almost 5 years ago

#31 - added `expand` option to `BinaryMap`

Pull Request - State: closed - Opened by jbloom almost 5 years ago

#30 - Fix bug in `AbstractEpistasis.preferences`

Pull Request - State: closed - Opened by jbloom almost 5 years ago

#29 - get mutational effects and preferences with more options

Pull Request - State: closed - Opened by jbloom about 5 years ago

#28 - Fix errors using `pandas.query` for ``nan`` values

Pull Request - State: closed - Opened by jbloom about 5 years ago

#27 - change recommendations for base in scores / phenotypes to prefs

Pull Request - State: closed - Opened by jbloom about 5 years ago

#26 - convert scores / phenotypes to preferences

Pull Request - State: closed - Opened by jbloom about 5 years ago

#25 - better caching for better pickling of epistasis models

Pull Request - State: closed - Opened by jbloom about 5 years ago

#24 - predict unseen variants example

Pull Request - State: closed - Opened by jbloom about 5 years ago

#23 - global epistasis likelihood more robust to experimental noise

Pull Request - State: closed - Opened by jbloom about 5 years ago

#22 - implement Cauchy likelihood, more robust to noise

Pull Request - State: closed - Opened by jbloom about 5 years ago

#21 - minor fixes to `codonvariant_sim_data.ipynb` example

Pull Request - State: closed - Opened by jbloom about 5 years ago

#20 - added global epistasis models and incremented to version 0.3.0

Pull Request - State: closed - Opened by jbloom about 5 years ago

#19 - update simulator to use enrichments

Pull Request - State: closed - Opened by jbloom about 5 years ago

#18 - speed up by fixing x in I-splines

Pull Request - State: closed - Opened by jbloom about 5 years ago

#17 - merge exact grad into epistasis

Pull Request - State: closed - Opened by jbloom about 5 years ago

#16 - remove deprecated `Bio.Alphabet` to fix warning

Pull Request - State: closed - Opened by jbloom about 5 years ago

#15 - Added `utils.tidy_to_corr`

Pull Request - State: closed - Opened by jbloom over 5 years ago

#14 - version 0.2.0 complete: docs updated, example notebooks

Pull Request - State: closed - Opened by jbloom over 5 years ago

#13 - add `syn_as_wt` to `CodonVariantTable.classifyVariants`

Pull Request - State: closed - Opened by jbloom over 5 years ago

#12 - fix bug w `sample_rename` in `CodonVariantTable.plotMutFreqs`

Pull Request - State: closed - Opened by jbloom over 5 years ago

#11 - `sample_rename` for `CodonVariantTable` plots

Pull Request - State: closed - Opened by jbloom over 5 years ago

#10 - better plotting

Pull Request - State: closed - Opened by jbloom over 5 years ago

#9 - added `CodonVariantTable.add_sample_counts_df` method

Pull Request - State: closed - Opened by jbloom over 5 years ago

#8 - `libraries` arg to `CodonVariantTable.func_scores`

Pull Request - State: closed - Opened by jbloom over 5 years ago

#7 - fix bug faceting samples in `CodonVariantTable`.

Pull Request - State: closed - Opened by jbloom over 5 years ago

#6 - Illumina barcode parser

Pull Request - State: closed - Opened by jbloom over 5 years ago

#5 - updates to .gitignore and test reqs

Pull Request - State: closed - Opened by jbloom over 5 years ago

#4 - specify subs col in init `CodonVariantTable`

Pull Request - State: closed - Opened by jbloom over 5 years ago

#3 - Make compatible with `pandas` 0.25

Pull Request - State: closed - Opened by jbloom over 5 years ago

#2 - add `CodonVariant.numCodonMutsByType` method

Pull Request - State: closed - Opened by jbloom over 5 years ago

#1 - Fixes to docs /formatting in Jupyter notebooks

Pull Request - State: closed - Opened by jbloom over 5 years ago