czbiohub-sf orpheum issues

czbiohub-sf / orpheum

Orpheum (Previously called and published under sencha) is a Python package for directly translating RNA-seq reads into coding protein sequence.

MIT License

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issues

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Add support for reading bam files

#107 olgabot opened 1 year ago
0
Accept 10x bam as input and output tagged bam

#106 olgabot opened 2 years ago
3
[Question] Use of Orpheum for non mammalian species ?

#105 RxLoutre opened 2 years ago
0
Output only noncoding reads in --noncoding-nucleotide-fasta

#104 taylorreiter opened 2 years ago
0
orpheum translate assigns all reads to non-coding with a jaccard index of 0

#103 taylorreiter opened 2 years ago
1
Fixing ci and fix tests incorporating Tessa's changes, fix sourmash minhash import

#102 pranathivemuri closed 2 years ago
0
fix click reporting arg specification

#101 bluegenes closed 2 years ago
2
boolean requirement leads to invalid value for '--csv' and '--parquet'

#100 taylorreiter closed 2 years ago
0
Update minimal sourmash version for different hash_murmur location

#99 olgabot opened 3 years ago
0
Missed suggestions from olga

#98 pranathivemuri closed 3 years ago
0
rename sencha to orpheum

#97 pranathivemuri closed 3 years ago
0
fix the bug in unique files of create_save_summary

#96 pranathivemuri closed 3 years ago
0
rename jaccard to containment

#95 pranathivemuri opened 3 years ago
0
rename sencha to leaftea

#94 pranathivemuri opened 3 years ago
0
Revert multiprocessing

#93 pranathivemuri closed 3 years ago
2
No spaces in output sequence name

#92 olgabot closed 3 years ago
2
Revert "multiprocessing for sencha translate"

#91 pranathivemuri closed 3 years ago
1
add pathos dependency for multiprocessing

#90 pranathivemuri closed 3 years ago
0
multiprocessing for sencha translate

#89 pranathivemuri closed 3 years ago
0
Add debugging and list based coding scores

#88 pranathivemuri closed 3 years ago
0
Output gzipped fasta files

#87 olgabot opened 3 years ago
1
Consider using "sourmash search --containment" for "translate"

#86 olgabot opened 3 years ago
1
sencha translate memory allocation error

#85 phoenixAja closed 3 years ago
6
add multiprocessing to sencha translate

#84 pranathivemuri closed 3 years ago
8
Parallelize "translate"

#83 olgabot closed 3 years ago
2
Remove Biopython dependency

#82 olgabot closed 4 years ago
2
Add more conveniences for noncoding nucleotide alphabets

#81 olgabot opened 4 years ago
0
add nucl mappings, slight reorg

#80 bluegenes opened 4 years ago
1
Consider using MyST for Sphinx-compatible Markdown documentation

#79 olgabot opened 4 years ago
1
What to do about B and Z amino acid letters?

#78 olgabot opened 4 years ago
0
Update to sourmash Nodegraph instead of khmer to allow for computation of minimum read length

#77 olgabot opened 4 years ago
1
Actually have documentation, either on readthedocs or github.io

#76 olgabot opened 4 years ago
0
option to output translate coding scores as parquet

#75 bluegenes closed 4 years ago
0
Indexing improvements

#74 olgabot closed 4 years ago
1
Warn users if the bloom filter table size is too small

#73 olgabot opened 4 years ago
0
Ignore k-mers with stop codons, Selenocysteine and other nontraditional amino acids

#72 olgabot opened 4 years ago
0
Add option to ignore short sequences when building an index

#71 olgabot opened 4 years ago
0
add github action for auto linting with black

#70 pranathivemuri opened 4 years ago
1
Create pull_request_template.md

#69 pranathivemuri closed 4 years ago
5
add option to output csv as parquet

#68 bluegenes closed 4 years ago
0
Black formatting

#67 bluegenes closed 4 years ago
5
build index from directory of peptide files

#66 bluegenes closed 4 years ago
7
Add k-mers size for each alphabet to usage

#65 olgabot closed 4 years ago
0
remove branch.yml

#64 pranathivemuri closed 4 years ago
1
add release doc for sencha

#63 pranathivemuri closed 4 years ago
1
How big of a bloom filter should one use?

#62 olgabot opened 4 years ago
1
rename khtools to sencha

#61 pranathivemuri closed 4 years ago
3
add tests for same read having coding, non-coding detected as coding …

#60 pranathivemuri closed 4 years ago
0
Update summary json with new csv

#59 olgabot closed 4 years ago
2
change translation frame type description

#58 pranathivemuri closed 4 years ago
6