Showing : ncbi • reset
8
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7
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3.4k
views
Generating a proper TxDb instance from NCBI GFF Annotations File
ncbi refseq maketxdbfromgff fetchExtendedChromInfoFromUCSC genomeinfodb
updated 8.2 years ago by 16k • written 8.3 years ago by ▴ 10
2
votes
4
replies
984
views
MakeOrgPackageFromNCBI SQL error
MakeOrgPackageFromNCBI NCBI SQL AnnotationForge
updated 3.9 years ago by 65k • written 3.9 years ago by • 0
2
votes
2
replies
3.2k
views
How to Normalize the Microarray Data Obtained from ncbi?
microarray normalization ncbi
updated 8.9 years ago by 65k • written 9.0 years ago by ▴ 20
2
votes
5
replies
733
views
Conversion between different types of bioinformatic forms. (eg. NCBI protein to Ensembl protein) in R
RStudio convert ensembldb NCBI
5 months ago j_denton • 0
2
votes
3
replies
471
views
NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
Rstudio cDNA ensembldb NCBI
4 months ago R_Page • 0
1
vote
5
replies
1.3k
views
Gene Ontology analysis
ontology edger limma ncbi organism package
updated 4.1 years ago by 50k • written 4.1 years ago by ▴ 20
0
votes
1
reply
1.2k
views
.getNcbiURL returns old NCBI url ?
annotate ncbi url
9.3 years ago reuma • 0
0
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0
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626
views
getGFFSet function CRASHES R session
getGFF NCBI biomartr biomaRt
2.7 years ago Matan G. ▴ 60
0
votes
4
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2.2k
views
Rsubread function buildindex cannot handle the GRCh38.p7 reference from NCBI
rsubread ncbi GRCh38 hg38
updated 7.5 years ago by ★ 3.6k • written 7.5 years ago by • 0
0
votes
0
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1.4k
views
Search SRA based on BioSample Attributes
ncbi sra search
8.2 years ago massacomgrao • 0
10 results • Page 1 of 1
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Comment: Estimating Cell Counts for EPIC V2 array data by normawiedman059 • 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
Comment: Finding DEGs by using edgeR by Gordon Smyth 50k
Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
Comment: How to make DGEList and design matrix by edgeR package by prity6459 • 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR by prity6459 • 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
Votes
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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