ratschlab/immunopepper issues and pull requests

#87 - Bump pyarrow from 0.17.1 to 14.0.1

Pull Request - State: open - Opened by dependabot[bot] 11 months ago
Labels: dependencies

#86 - The make_bg module is not found

Issue - State: open - Opened by Xutainbing 11 months ago - 1 comment

#85 - Feature/refactor

Pull Request - State: open - Opened by lthp 12 months ago

#84 - Fix/minor

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

#83 - Documentation

Pull Request - State: closed - Opened by pilarbc123 over 1 year ago

#82 - Feature/filtering gzip

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

#81 - Revert "Lighterweight simplify write legacypartitions"

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

#80 - Fix/postpone expression extraction

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

#79 - Lighterweight simplify write legacypartitions

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

#78 - Feature/lighterweight

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

#77 - Experimental/global variables

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

#76 - Feature/rf flag refine

Pull Request - State: closed - Opened by lthp about 2 years ago - 2 comments

#75 - Fix/do not repeat yourself

Pull Request - State: closed - Opened by lthp about 2 years ago

#74 - Fix/features improvements

Pull Request - State: closed - Opened by lthp about 2 years ago

#73 - Fix/rf flag

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

#72 - Fix/junction expression

Pull Request - State: closed - Opened by lthp over 2 years ago - 1 comment

#71 - Clean up mutations.py. Add tests. Remove redundant --mutation_mode parameter.

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

#70 - Clean up _io.py: add comments and simplify code. No tests.

Pull Request - State: closed - Opened by danieldanciu over 2 years ago - 1 comment

#69 - Clean up filter.py, add tests and update code documentation

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

#68 - Clean up the cpython dna to peptide translator and add tests

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

#67 - Clean up config.py, fix typos in documentation and fix requirements.txt

Pull Request - State: closed - Opened by danieldanciu over 2 years ago - 1 comment

#66 - Bump psutil from 5.4.6 to 5.6.6

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#65 - Feature/kmer structure dict validated develop mmt mx stat

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

#64 - immunopepper memory still an issue

Issue - State: closed - Opened by PhilippMarkolin about 4 years ago

#63 - Feature/parallel

Pull Request - State: closed - Opened by akahles over 4 years ago - 1 comment

#62 - Cleanup

Pull Request - State: closed - Opened by akahles over 4 years ago - 1 comment

#61 - First set of speedups

Pull Request - State: closed - Opened by akahles over 4 years ago - 1 comment

#60 - Feature/map kmer to seq

Pull Request - State: closed - Opened by corn23 over 4 years ago

#59 - Hotfix/fix readme typo

Pull Request - State: closed - Opened by corn23 over 4 years ago

#58 - get_idx error

Issue - State: closed - Opened by PhilippMarkolin over 4 years ago - 10 comments

#57 - Feature/deal with more filters

Pull Request - State: closed - Opened by corn23 over 4 years ago

#56 - Hotfix/update readme for mouse data

Pull Request - State: closed - Opened by corn23 over 4 years ago

#55 - Hotfix/fix the metadata headerline

Pull Request - State: closed - Opened by corn23 over 4 years ago

#54 - hotfix/add_warning

Pull Request - State: closed - Opened by corn23 over 4 years ago

#53 - Development

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

#52 - make changes to the description of output files in build mode

Pull Request - State: closed - Opened by corn23 almost 5 years ago

#51 - Feature/cleanup

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

#50 - Feature/change output

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

#49 - Feature/release2 patch

Pull Request - State: closed - Opened by corn23 almost 5 years ago

#48 - Feature/change output

Pull Request - State: closed - Opened by corn23 almost 5 years ago

#47 - Modify the gene expression data on the fly

Issue - State: open - Opened by corn23 almost 5 years ago

#46 - Output file in compressed format

Issue - State: closed - Opened by corn23 almost 5 years ago - 1 comment

#45 - Bugfix/python2

Pull Request - State: closed - Opened by akahles almost 5 years ago - 2 comments

#44 - AttributeError: 'numpy.ndarray' object has no attribute 'decode'

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

#43 - Module not found Error in immunopepper_build.py

Issue - State: closed - Opened by PhilippMarkolin about 5 years ago - 2 comments

#42 - cPickle and python3

Issue - State: closed - Opened by PhilippMarkolin about 5 years ago - 1 comment

#41 - module not found error

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

#40 - fix a bug: output is_crossjunction flag even without count file

Pull Request - State: closed - Opened by corn23 about 5 years ago

#39 - Hotfix/fix single gene expression test file

Pull Request - State: closed - Opened by corn23 about 5 years ago

#38 - Interface changes

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

#37 - Add a flag to choose between adding a new column or generating a new file in immunopepper diff mode

Issue - State: closed - Opened by corn23 about 5 years ago

#36 - replace print statement using logging

Issue - State: closed - Opened by izcram about 5 years ago - 1 comment

#35 - Feature/add new parser

Pull Request - State: closed - Opened by corn23 about 5 years ago

#34 - junctionOI_flag issue

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

#33 - Indexing sample id in count file

Issue - State: closed - Opened by corn23 over 5 years ago

#32 - Feature/output separate gene expression file

Pull Request - State: closed - Opened by corn23 over 5 years ago

#31 - Remove the assertion in checking if somatic mutations are consistency.

Pull Request - State: closed - Opened by corn23 over 5 years ago

#30 - Feature needed - retrieve gene expression list for each sample

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

#29 - add constraint to the coord so that stop always greater than start

Pull Request - State: closed - Opened by corn23 over 5 years ago

#28 - Feature/write pep on the fly

Pull Request - State: closed - Opened by corn23 over 5 years ago

#27 - Integrate more parsing options

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

#26 - PRIORITY +++++: Reduce libsize set to protein coding

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

#25 - don't output empty string

Pull Request - State: closed - Opened by corn23 over 5 years ago

#24 - Hotfix/change kmer output

Pull Request - State: closed - Opened by corn23 over 5 years ago

#23 - resolve libsize output bug (do not new a expression list before)

Pull Request - State: closed - Opened by corn23 over 5 years ago

#22 - Not output short kmer

Issue - State: closed - Opened by corn23 over 5 years ago

#21 - infer chromosome name from annotation file

Issue - State: closed - Opened by corn23 over 5 years ago

#20 - Wrong warning messages

Issue - State: closed - Opened by corn23 over 5 years ago - 1 comment

#19 - processed genes takes too much memory

Issue - State: closed - Opened by corn23 over 5 years ago

#18 - the libsize is False

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

#17 - Feature/dev python3

Pull Request - State: closed - Opened by corn23 over 5 years ago - 2 comments

#16 - deal with mismatch sample id

Issue - State: closed - Opened by corn23 over 5 years ago

#15 - cross_junction field missing in concat file

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

#14 - Feature/dev python3 testing

Pull Request - State: closed - Opened by corn23 over 5 years ago

#13 - Feature/output background

Pull Request - State: closed - Opened by corn23 over 5 years ago - 1 comment

#12 - Prepare release

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

#11 - Merge candidate

Pull Request - State: closed - Opened by corn23 almost 6 years ago

#10 - Merge candidate

Pull Request - State: closed - Opened by corn23 almost 6 years ago

#9 - use generator in get_effective_lines

Issue - State: closed - Opened by izcram almost 6 years ago - 1 comment

#8 - Merge candidate

Pull Request - State: closed - Opened by corn23 almost 6 years ago

#7 - Feature/entry point and install doc

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

#6 - Feature/add insertion

Pull Request - State: closed - Opened by corn23 about 6 years ago

#5 - add the required test file

Pull Request - State: closed - Opened by corn23 about 6 years ago

#4 - adding circleci configuration

Pull Request - State: closed - Opened by izcram about 6 years ago

#3 - Development fix bug

Pull Request - State: closed - Opened by corn23 about 6 years ago - 2 comments

#2 - Development fix bug

Pull Request - State: closed - Opened by corn23 about 6 years ago

#1 - Fix/env cleanup

Pull Request - State: closed - Opened by izcram about 6 years ago

GitHub / ratschlab/immunopepper issues and pull requests