Ecosyste.ms: Issues

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

GitHub / czbiohub/orpheum issues and pull requests

#107 - Add support for reading bam files

Pull Request - State: open - Opened by olgabot over 2 years ago

#106 - Accept 10x bam as input and output tagged bam

Issue - State: open - Opened by olgabot over 2 years ago - 3 comments

#105 - [Question] Use of Orpheum for non mammalian species ?

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

#101 - fix click reporting arg specification

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

#99 - Update minimal sourmash version for different hash_murmur location

Pull Request - State: open - Opened by olgabot almost 4 years ago

#98 - Missed suggestions from olga

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

#97 - rename sencha to orpheum

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

#96 - fix the bug in unique files of create_save_summary

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

#95 - rename jaccard to containment

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

#94 - rename sencha to leaftea

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

#93 - Revert multiprocessing

Pull Request - State: closed - Opened by pranathivemuri over 4 years ago - 2 comments

#92 - No spaces in output sequence name

Pull Request - State: closed - Opened by olgabot over 4 years ago - 2 comments

#91 - Revert "multiprocessing for sencha translate"

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

#90 - add pathos dependency for multiprocessing

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

#89 - multiprocessing for sencha translate

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

#88 - Add debugging and list based coding scores

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

#87 - Output gzipped fasta files

Issue - State: open - Opened by olgabot over 4 years ago - 1 comment

#86 - Consider using "sourmash search --containment" for "translate"

Issue - State: open - Opened by olgabot over 4 years ago - 1 comment

#85 - sencha translate memory allocation error

Issue - State: closed - Opened by phoenixAja over 4 years ago - 6 comments

#84 - add multiprocessing to sencha translate

Pull Request - State: closed - Opened by pranathivemuri over 4 years ago - 8 comments

#83 - Parallelize "translate"

Issue - State: closed - Opened by olgabot over 4 years ago - 2 comments

#82 - Remove Biopython dependency

Pull Request - State: closed - Opened by olgabot over 4 years ago - 2 comments

#81 - Add more conveniences for noncoding nucleotide alphabets

Pull Request - State: open - Opened by olgabot over 4 years ago

#80 - add nucl mappings, slight reorg

Pull Request - State: open - Opened by bluegenes over 4 years ago - 1 comment

#79 - Consider using MyST for Sphinx-compatible Markdown documentation

Issue - State: open - Opened by olgabot over 4 years ago - 1 comment

#78 - What to do about B and Z amino acid letters?

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

#75 - option to output translate coding scores as parquet

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

#74 - Indexing improvements

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

#73 - Warn users if the bloom filter table size is too small

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

#71 - Add option to ignore short sequences when building an index

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

#70 - add github action for auto linting with black

Issue - State: open - Opened by pranathivemuri over 4 years ago - 1 comment

#69 - Create pull_request_template.md

Pull Request - State: closed - Opened by pranathivemuri over 4 years ago - 5 comments

#68 - add option to output csv as parquet

Issue - State: closed - Opened by bluegenes over 4 years ago

#67 - Black formatting

Pull Request - State: closed - Opened by bluegenes over 4 years ago - 5 comments

#66 - build index from directory of peptide files

Pull Request - State: closed - Opened by bluegenes over 4 years ago - 7 comments

#65 - Add k-mers size for each alphabet to usage

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

#64 - remove branch.yml

Pull Request - State: closed - Opened by pranathivemuri almost 5 years ago - 1 comment

#63 - add release doc for sencha

Pull Request - State: closed - Opened by pranathivemuri almost 5 years ago - 1 comment

#62 - How big of a bloom filter should one use?

Issue - State: open - Opened by olgabot almost 5 years ago - 1 comment

#61 - rename khtools to sencha

Pull Request - State: closed - Opened by pranathivemuri almost 5 years ago - 3 comments

#59 - Update summary json with new csv

Issue - State: closed - Opened by olgabot almost 5 years ago - 2 comments
Labels: bug

#58 - change translation frame type description

Pull Request - State: closed - Opened by pranathivemuri almost 5 years ago - 6 comments

#57 - actually fix the csv bug

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

#56 - extract coding csv fix

Pull Request - State: closed - Opened by pranathivemuri almost 5 years ago - 1 comment

#55 - Add sonarcloud code quality/smell analysis

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

#54 - Add pytest.fixture to peptide_bloom_filter_single_read

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

#53 - [MRG] Refactoring extract_Coding

Pull Request - State: closed - Opened by pranathivemuri almost 5 years ago - 3 comments

#51 - Add --sensitive and --specific flags to "translate"

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

#50 - Rename/alias "extract-coding" to "translate"

Issue - State: closed - Opened by olgabot almost 5 years ago - 2 comments

#49 - More strict coding/noncoding filters

Pull Request - State: open - Opened by olgabot almost 5 years ago - 1 comment

#48 - Valid translation frames shouldn't be from opposite strands

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

#47 - Add protein k-mer counting

Pull Request - State: open - Opened by olgabot almost 5 years ago

#46 - More strict filtering of low-complexity sequences

Issue - State: open - Opened by olgabot almost 5 years ago - 1 comment
Labels: enhancement

#44 - Rename/alias `bloom-filter` to `index`?

Issue - State: closed - Opened by olgabot almost 5 years ago - 1 comment
Labels: enhancement, help wanted

#43 - Use GitHub actions for testing

Pull Request - State: closed - Opened by olgabot almost 5 years ago - 1 comment

#42 - Refactor extract_coding to be object oriented

Issue - State: closed - Opened by olgabot almost 5 years ago - 2 comments

#41 - Change to GitHub Actions for testing

Issue - State: closed - Opened by olgabot almost 5 years ago

#39 - Support all-by-all comparison for noncoding / nucleotides

Issue - State: open - Opened by olgabot almost 5 years ago
Labels: enhancement

#38 - Rename to .. something else

Issue - State: closed - Opened by olgabot almost 5 years ago - 5 comments

#36 - Make a 1.0.0 release!!

Issue - State: closed - Opened by olgabot almost 5 years ago - 3 comments

#35 - bug in extract coding

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

#34 - Olgabot/fix empty predict coding

Pull Request - State: closed - Opened by olgabot almost 5 years ago - 1 comment

#33 - Failure if input file is empty

Issue - State: closed - Opened by olgabot almost 5 years ago

#32 - Add new false positive rate calculation

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

#31 - Get protein-coding sensitivity/specificity of extract_coding

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

#30 - BUG: coding_scores.csv for extract_coding isn't accurate for the number of frames per sample

Issue - State: closed - Opened by olgabot almost 5 years ago - 11 comments
Labels: bug

#29 - Ideal k-mer sizes by alphabet size

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

#28 - constrain peptide-ksize to int

Pull Request - State: closed - Opened by bluegenes almost 5 years ago - 1 comment

#27 - Add an "eject" option for k-mer comparison

Issue - State: closed - Opened by olgabot almost 5 years ago

#26 - Revert "long read translation added"

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

#25 - Convert pandas/apache parquet to vaex-compatible format

Pull Request - State: closed - Opened by olgabot about 5 years ago - 2 comments

#24 - More Encodings + kmer comparison CLI

Pull Request - State: closed - Opened by olgabot about 5 years ago - 1 comment

#23 - DO NOT MERGE -- Franken-branch of kmer comparison CLI + more encodings

Pull Request - State: closed - Opened by olgabot about 5 years ago - 2 comments

#22 - CLI for comparing k-mer content of many fastas across ksizes and alphabets

Pull Request - State: closed - Opened by olgabot about 5 years ago - 3 comments

#21 - Actually test the numerical encodings

Pull Request - State: closed - Opened by olgabot about 5 years ago - 1 comment

#20 - Use provided coding peptides to make test bloom filter set

Pull Request - State: closed - Opened by olgabot about 5 years ago - 1 comment

#19 - More encodings + long reads

Pull Request - State: closed - Opened by olgabot about 5 years ago - 1 comment

#18 - long read translation added

Pull Request - State: closed - Opened by pranathivemuri about 5 years ago - 3 comments

#17 - Rust-ify "translate"

Issue - State: open - Opened by olgabot about 5 years ago - 2 comments
Labels: enhancement, help wanted

#15 - Fix click stderr output

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

#14 - Allow for k-mer comparison of many fasta proteomes

Issue - State: open - Opened by olgabot about 5 years ago - 1 comment
Labels: enhancement

#13 - Use extract_kmers rust module to count protein k-mers

Issue - State: open - Opened by olgabot about 5 years ago
Labels: enhancement

#12 - CLI for k-mer homology

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

#10 - Expand extract_coding to work on long reads

Issue - State: open - Opened by olgabot over 5 years ago
Labels: enhancement

#9 - Add multiqc module

Issue - State: open - Opened by olgabot over 5 years ago - 3 comments
Labels: enhancement

#5 - Deplete species-specific signal with TF-IDF

Pull Request - State: closed - Opened by olgabot almost 6 years ago - 3 comments

#3 - Fix relative imports

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

#1 - Globally replace kh-tools --> khtools

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