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Hi Alex
I have been trying to generate index for Danio rerio using these fasta and gff3 file:
http://ftp.ensembl.org/pub/current_gff3/danio_rerio/Danio_rerio.GRCz11.103.chr.gff3.gz
http://ftp.ensem…
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See https://github.com/auerbachs/BMDExpress-2/wiki/Additional-Information#supported-microarrays
Current list should be:
|ID |…
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R version
4.3.1
packageVersion("clusterProfiler")
‘4.10.1’
get_wp_organisms() gives:
"Caenorhabditis elegans" "Bos taurus" "Arabidopsis thaliana"
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https://docs.google.com/document/d/1JJ8s-YMOoNZQ-gQ-YqL5vTlxbXcbuTaqyHpuZkMSQkI/edit#heading=h.9qvpznubphjs
```
GenomeFeature(chromosome='3',gene='sox9b',genome='Danio rerio',title='sox9b',highlig…
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Hi,
I am trying to extract SNPs using hisat2_extract_snps_haplotypes_VCF.py script from Ensembl VCF file (ftp://ftp.ensembl.org/pub/release-87/variation/vcf/danio_rerio/Danio_rerio.vcf.gz) to build…
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Hi! Thank you for this great software.
I was wondering if you plan to include other models or a code for building the necessary IPA reference?
I work with danio rerio and would love to use InPACT…
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[2023-09-20T09:48:26+0800] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
[2023-09-20T09:48:26+0800] [MainThread] [I] [toil] Running Toil version 5.12.0-6d5a5b83b649cd8adf34a5cfe…
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Currently the phenodigm score generation relies on some old datasets located in monarch-initiative/monarch-owlsim-data.
@kshefchek What should these be replaced with:
```
# OWLSIM DATA
MONARCH…
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I'm having troubles with ensDbFromGff for some gff3 files downloaded from Ensembl ftp. For example, Danio rerio in Ensembl versions 94, 95, and 96 (but not Ensembl versions 93, 92, 91, 90, or 85), usi…
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Based upon previous exploration of the data, I suspect that some cells with high cell cycle related gene expression are being called as doublets (likely because I have 2 or 3 different clusters that a…