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czbiohub-sf
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nf-predictorthologs
*de novo* orthologous gene predictions from bam + bed or fasta/fastq data
MIT License
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Only support diff hash with aligned/unaligned and sourmash search for now
#42
olgabot
closed
4 years ago
2
Filter bam with hashes, do featurecounts orthology (for real this time)
#41
olgabot
closed
3 years ago
2
Don't require signatures to be separated by aligned/unaligned
#40
olgabot
opened
4 years ago
1
Add ripgrep
#39
olgabot
closed
4 years ago
2
Add subread and bioawk
#38
olgabot
closed
4 years ago
0
diffhash updates
#37
olgabot
closed
4 years ago
2
Only do sourmash search on unaligned hashes
#36
olgabot
closed
4 years ago
3
Add option to use sourmash to search instead of diamond
#35
olgabot
closed
4 years ago
2
Update zip, rsync dependencies + Makefile
#34
olgabot
closed
4 years ago
1
Add reads csv input option
#33
bluegenes
closed
4 years ago
3
Potentially use kaamer instead of diamond
#32
olgabot
opened
4 years ago
1
olgabot/diff hash expression dependencies v2
#31
olgabot
closed
4 years ago
1
Add parser to summarize diamond output
#30
olgabot
opened
4 years ago
1
Add jupyter and s3fs dependencies for khtools
#29
olgabot
closed
4 years ago
0
Add step to filter for only NP_ sequences from NCBI
#28
olgabot
opened
4 years ago
0
Add dependencies for differential hash expression
#27
olgabot
closed
4 years ago
0
Differential hash expression
#26
olgabot
closed
4 years ago
2
Input hashes + protein sequences
#25
olgabot
closed
4 years ago
4
Update sourmash, khtools dependencies
#24
olgabot
closed
4 years ago
0
Add documentation
#23
olgabot
opened
4 years ago
0
Support noncoding RNA search with Infernal on Rfam
#22
olgabot
closed
4 years ago
1
Support input of DNA or protein fasta files
#21
olgabot
opened
4 years ago
0
Fix whitespace in bam + bed PR
#20
olgabot
closed
4 years ago
0
Support input of multiple bam files with `--bam '*{.bam,.bam.bai}'`
#19
olgabot
opened
4 years ago
0
Test single vs paired end bam files
#18
olgabot
opened
4 years ago
0
samtools view fastq updates
#17
olgabot
closed
4 years ago
0
Add rsync to dependencies
#16
olgabot
closed
4 years ago
0
Add option to skip FastQC and trimming
#15
olgabot
opened
4 years ago
0
Conda unzip incompatible with NCBI's taxdmp.zip
#14
olgabot
closed
4 years ago
2
Merge nf-core 1.9 template updates
#13
olgabot
closed
4 years ago
1
Update dependencies
#12
olgabot
closed
4 years ago
2
Phoenix/bam bed intersect
#11
phoenixAja
closed
4 years ago
3
Support input of multiple bed files
#10
olgabot
opened
4 years ago
0
Test pull request
#9
ewels
closed
4 years ago
0
Testing actions branch checks
#8
ewels
closed
4 years ago
1
Add rsync, unzip dependencies
#7
olgabot
closed
4 years ago
0
Update MultiQC and khtools dependencies
#6
olgabot
closed
4 years ago
0
Add MultiQC for khtools
#5
olgabot
opened
4 years ago
1
Update Dockerfile and environment
#4
olgabot
closed
4 years ago
0
Support input of CSVs to groupby sample ids, extract coding, compute signatures, get shared hashes, convert to k-mers
#3
olgabot
closed
4 years ago
1
Support input of bam + bed file
#2
olgabot
closed
4 years ago
0
Initial setup for predicting orthologs
#1
olgabot
closed
4 years ago
2
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