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czbiohub-sf
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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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actually fix the csv bug
#57
pranathivemuri
closed
4 years ago
0
extract coding csv fix
#56
pranathivemuri
closed
4 years ago
1
Add sonarcloud code quality/smell analysis
#55
olgabot
opened
4 years ago
0
Add pytest.fixture to peptide_bloom_filter_single_read
#54
olgabot
closed
4 years ago
0
[MRG] Refactoring extract_Coding
#53
pranathivemuri
closed
4 years ago
3
Revamp indexing and translating to use multiple bloom filters of different encodings and ksizes
#52
olgabot
opened
4 years ago
0
Add --sensitive and --specific flags to "translate"
#51
olgabot
opened
4 years ago
0
Rename/alias "extract-coding" to "translate"
#50
olgabot
closed
4 years ago
2
More strict coding/noncoding filters
#49
olgabot
opened
4 years ago
1
Valid translation frames shouldn't be from opposite strands
#48
olgabot
opened
4 years ago
0
Add protein k-mer counting
#47
olgabot
opened
4 years ago
0
More strict filtering of low-complexity sequences
#46
olgabot
opened
4 years ago
1
Use XOR filter instead of bloom filter for storing reference proteome
#45
olgabot
opened
4 years ago
0
Rename/alias `bloom-filter` to `index`?
#44
olgabot
closed
4 years ago
1
Use GitHub actions for testing
#43
olgabot
closed
4 years ago
1
Refactor extract_coding to be object oriented
#42
olgabot
closed
4 years ago
2
Change to GitHub Actions for testing
#41
olgabot
closed
4 years ago
0
Provide pre-computed bloom filters for extracting protein coding
#40
olgabot
opened
4 years ago
0
Support all-by-all comparison for noncoding / nucleotides
#39
olgabot
opened
4 years ago
0
Rename to .. something else
#38
olgabot
closed
4 years ago
5
read_id in coding peptides output if not using precomputed peptide bloom filter
#37
bluegenes
opened
4 years ago
0
Make a 1.0.0 release!!
#36
olgabot
closed
4 years ago
3
bug in extract coding
#35
pranathivemuri
closed
4 years ago
5
Olgabot/fix empty predict coding
#34
olgabot
closed
4 years ago
1
Failure if input file is empty
#33
olgabot
closed
4 years ago
0
Add new false positive rate calculation
#32
olgabot
closed
4 years ago
0
Get protein-coding sensitivity/specificity of extract_coding
#31
olgabot
opened
4 years ago
0
BUG: coding_scores.csv for extract_coding isn't accurate for the number of frames per sample
#30
olgabot
closed
4 years ago
11
Ideal k-mer sizes by alphabet size
#29
olgabot
closed
4 years ago
0
constrain peptide-ksize to int
#28
bluegenes
closed
4 years ago
1
Add an "eject" option for k-mer comparison
#27
olgabot
closed
4 years ago
0
Revert "long read translation added"
#26
pranathivemuri
closed
4 years ago
0
Convert pandas/apache parquet to vaex-compatible format
#25
olgabot
closed
4 years ago
2
More Encodings + kmer comparison CLI
#24
olgabot
closed
4 years ago
1
DO NOT MERGE -- Franken-branch of kmer comparison CLI + more encodings
#23
olgabot
closed
4 years ago
2
CLI for comparing k-mer content of many fastas across ksizes and alphabets
#22
olgabot
closed
4 years ago
3
Actually test the numerical encodings
#21
olgabot
closed
4 years ago
1
Use provided coding peptides to make test bloom filter set
#20
olgabot
closed
4 years ago
1
More encodings + long reads
#19
olgabot
closed
4 years ago
1
long read translation added
#18
pranathivemuri
closed
4 years ago
3
Rust-ify "translate"
#17
olgabot
opened
4 years ago
2
Add more sequence encodings
#16
olgabot
closed
4 years ago
1
Fix click stderr output
#15
olgabot
closed
4 years ago
0
Allow for k-mer comparison of many fasta proteomes
#14
olgabot
opened
4 years ago
1
Use extract_kmers rust module to count protein k-mers
#13
olgabot
opened
4 years ago
0
CLI for k-mer homology
#12
olgabot
closed
4 years ago
2
needed a few more requirements
#11
bluegenes
closed
4 years ago
2
Expand extract_coding to work on long reads
#10
olgabot
opened
4 years ago
0
Add multiqc module
#9
olgabot
opened
4 years ago
3
Partition reads to coding, noncoding and low complexity
#8
olgabot
closed
4 years ago
10
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