Showing : NCBI • reset
2
votes
3
replies
1.1k
views
NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
Rstudio cDNA ensembldb NCBI
2.0 years ago R_Page • 0
4
votes
6
replies
3.6k
views
Conversion between different types of bioinformatic forms. (eg. NCBI protein to Ensembl protein) in R
RStudio convert ensembldb NCBI
updated 14 months ago by • 0 • written 2.1 years ago by • 0
0
votes
0
replies
1.0k
views
getGFFSet function CRASHES R session
getGFF NCBI biomartr biomaRt
4.3 years ago Matan G. ▴ 60
2
votes
4
replies
1.5k
views
MakeOrgPackageFromNCBI SQL error
MakeOrgPackageFromNCBI NCBI SQL AnnotationForge
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
1
vote
5
replies
2.0k
views
Gene Ontology analysis
ontology edger limma ncbi organism package
updated 5.7 years ago by 53k • written 5.7 years ago by ▴ 20
0
votes
4
replies
2.8k
views
Rsubread function buildindex cannot handle the GRCh38.p7 reference from NCBI
rsubread ncbi GRCh38 hg38
updated 9.1 years ago by ★ 3.6k • written 9.1 years ago by • 0
0
votes
0
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1.8k
views
Search SRA based on BioSample Attributes
ncbi sra search
9.9 years ago massacomgrao • 0
8
votes
7
replies
4.6k
views
Generating a proper TxDb instance from NCBI GFF Annotations File
ncbi refseq maketxdbfromgff fetchExtendedChromInfoFromUCSC genomeinfodb
updated 9.9 years ago by 16k • written 9.9 years ago by ▴ 10
2
votes
2
replies
4.0k
views
How to Normalize the Microarray Data Obtained from ncbi?
microarray normalization ncbi
updated 10.6 years ago by 68k • written 10.6 years ago by ▴ 20
0
votes
1
reply
1.6k
views
.getNcbiURL returns old NCBI url ?
annotate ncbi url
10.9 years ago reuma • 0
10 results • Page 1 of 1
Recent ...
Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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