Ecosyste.ms: Issues

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GitHub / afrendeiro/toolkit issues and pull requests

#69 - PEP2 upgrade - KeyError getting bigwig (not a sample_attr)

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

#68 - fixed bug with overwrite flag

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

#67 - Bug if no significant results (e.g. from meme)

Issue - State: open - Opened by fwzhao over 4 years ago

#66 - Issue with calling subprocess command

Issue - State: open - Opened by fwzhao over 4 years ago - 2 comments

#65 - Call to `lola` passes bed_file without checking for timestamp

Issue - State: closed - Opened by afrendeiro over 4 years ago
Labels: bug

#64 - Function call to `homer_motifs` has wrong keyword-argument

Issue - State: open - Opened by afrendeiro over 4 years ago
Labels: bug

#63 - Motif vs. Meme

Issue - State: closed - Opened by fwzhao almost 5 years ago - 1 comment

#62 - Bug in structure of for loop iterating through gene_set_librar(ies)

Issue - State: closed - Opened by fwzhao almost 5 years ago - 1 comment

#61 - Enrichr step of run_enrichment_jobs missing time

Issue - State: closed - Opened by fwzhao about 5 years ago
Labels: bug

#60 - Bug in fisher test (differential overlap)

Issue - State: closed - Opened by fwzhao about 5 years ago
Labels: bug

#59 - Incorrect inference of multi-index in the case of non-str index

Issue - State: closed - Opened by fwzhao about 5 years ago - 3 comments
Labels: bug, wontfix

#58 - typo in attr name (organism)

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

#56 - Inconsisent shape of region_annotation vs. region_annotation_b

Issue - State: open - Opened by fwzhao about 5 years ago

#55 - Quick-fix: extra (inconsequential) comma

Issue - State: closed - Opened by fwzhao about 5 years ago

#54 - ATACAnalysis feature request - make chrom_state_file / build more explicit

Issue - State: closed - Opened by fwzhao about 5 years ago - 2 comments
Labels: enhancement

#53 - pybedtools - bedtool cannot turn into dataframe if NAs present in intersect result

Issue - State: closed - Opened by fwzhao about 5 years ago - 2 comments
Labels: bug

#52 - Typo in Example https://ngs-toolkit.readthedocs.io/en/latest/examples.html

Issue - State: closed - Opened by sreichl over 5 years ago - 1 comment

#51 - Dev

Pull Request - State: closed - Opened by afrendeiro over 5 years ago - 1 comment

#50 - more tests

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

#49 - v0.12

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

#48 - divvy 0.4.0 not supported

Issue - State: closed - Opened by afrendeiro over 5 years ago
Labels: bug

#47 - Allow initialization of subprojects when using `Analysis.from_pep()`

Issue - State: closed - Opened by afrendeiro over 5 years ago - 1 comment
Labels: enhancement

#46 - Dev

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

#45 - Merge from dev

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

#44 - plot_peak_characteristics error: Initializing dataframe with iterator

Issue - State: closed - Opened by fwzhao over 5 years ago - 1 comment

#43 - Might be a bug: actually want to reduce to .unique() values

Issue - State: closed - Opened by fwzhao over 5 years ago - 1 comment

#42 - numpy version might be too low

Issue - State: closed - Opened by fwzhao over 5 years ago - 1 comment

#41 - Merge from dev

Pull Request - State: closed - Opened by afrendeiro almost 6 years ago

#40 - Add own exceptions

Issue - State: open - Opened by afrendeiro almost 6 years ago
Labels: enhancement

#39 - Package name

Issue - State: open - Opened by afrendeiro almost 6 years ago

#38 - add CNV data generation for CNV module testing

Issue - State: open - Opened by afrendeiro almost 6 years ago
Labels: tests

#37 - test coverage (>=60%)

Issue - State: open - Opened by afrendeiro almost 6 years ago
Labels: enhancement, tests

#36 - full Python 2 and 3 support + testing

Issue - State: closed - Opened by afrendeiro almost 6 years ago - 1 comment
Labels: enhancement, tests

#35 - full cross-system independence (including job support)

Issue - State: closed - Opened by afrendeiro almost 6 years ago - 1 comment
Labels: enhancement

#34 - cross-package args/kwarg consistency

Issue - State: closed - Opened by afrendeiro almost 6 years ago
Labels: enhancement

#32 - PCA testing + plotting + enrichment of significant feature weights

Issue - State: open - Opened by afrendeiro almost 6 years ago
Labels: new feature

#31 - compartmentalization/redistribution of small functions in general to utils, graphics

Issue - State: closed - Opened by afrendeiro almost 6 years ago
Labels: enhancement, api

#30 - all high-level functions under Analysis

Issue - State: closed - Opened by afrendeiro almost 6 years ago
Labels: api

#29 - Independence of reference files

Pull Request - State: closed - Opened by afrendeiro almost 6 years ago

#28 - Fix bug collecting lola results when in serial mode

Pull Request - State: closed - Opened by afrendeiro almost 6 years ago

#27 - Add a Codacy badge to README.md

Pull Request - State: closed - Opened by codacy-badger almost 6 years ago

#26 - markdown readme doesn't render on pypi

Issue - State: closed - Opened by nsheff about 6 years ago - 1 comment

#25 - Implement GWAS enrichment analysis

Issue - State: open - Opened by afrendeiro about 6 years ago

#23 - plot differential enrichment enhancements

Pull Request - State: closed - Opened by fwzhao over 6 years ago - 2 comments

#22 - modified plot_differential_enrichment (plus some autopep8 formatting)

Pull Request - State: closed - Opened by fwzhao over 6 years ago - 1 comment

#21 - Implement HOMER motif analysis through de novo discovery, reduction and overrepresentation

Issue - State: closed - Opened by afrendeiro over 6 years ago - 3 comments
Labels: new feature

#19 - R dataframe conversion bugs

Issue - State: closed - Opened by fwzhao over 6 years ago - 3 comments
Labels: bug, enhancement

#18 - ddd

Issue - State: closed - Opened by fwzhao over 6 years ago

#17 - Does not replace hyphen ('-'), needs regex=True for Dataframe.replace()

Issue - State: closed - Opened by fwzhao over 6 years ago - 2 comments
Labels: bug, enhancement

#16 - TrackDb.txt sample group indentation

Issue - State: open - Opened by fwzhao over 6 years ago - 5 comments

#15 - fixed pca bug

Pull Request - State: closed - Opened by fwzhao over 6 years ago

#14 - Redirect atac_analysis.unsupervised to general.unsupervised

Issue - State: closed - Opened by fwzhao over 6 years ago - 1 comment

#13 - fixed bug in variable name (index in indices) in for loop

Pull Request - State: closed - Opened by afrendeiro over 6 years ago

#12 - Compare quantile normalization implementations and default to a native Python implementation

Issue - State: closed - Opened by afrendeiro over 6 years ago - 1 comment
Labels: enhancement

#11 - Handle sample and group attributes between functions better

Issue - State: closed - Opened by afrendeiro over 6 years ago
Labels: enhancement

#10 - Allow custom header in dataframes loaded by `load_data`

Issue - State: closed - Opened by afrendeiro almost 7 years ago
Labels: enhancement

#9 - Have functions from Analysis objects declaring their output

Issue - State: closed - Opened by afrendeiro almost 7 years ago - 1 comment
Labels: enhancement

#8 - Standardize use of "static/external" files in analysis

Issue - State: closed - Opened by afrendeiro about 7 years ago - 1 comment
Labels: enhancement

#7 - general.plot_differential fails getting groups when comparisons made are all-vs-all

Issue - State: closed - Opened by afrendeiro about 7 years ago - 1 comment
Labels: bug

#6 - Accommodate different lola output file formats (like tsv)

Issue - State: closed - Opened by fwzhao about 7 years ago - 1 comment

#5 - general module's collect_enrichment function not skipping homer properly

Issue - State: closed - Opened by fwzhao about 7 years ago - 1 comment
Labels: bug

#4 - rpy2 version not being enforced at installation

Issue - State: closed - Opened by afrendeiro about 7 years ago - 1 comment
Labels: bug

#3 - Recipes

Issue - State: closed - Opened by afrendeiro about 7 years ago - 1 comment

#2 - Change mkprj program into projectmanager

Issue - State: closed - Opened by afrendeiro about 7 years ago

#1 - Separate ngs_toolkit.general into more specific modules

Issue - State: closed - Opened by afrendeiro about 7 years ago - 1 comment
Labels: duplicate