6
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11
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4.0k
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How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 9 weeks ago by • 0 • written 3.2 years ago by ▴ 40
6
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5
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1.2k
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error message when I use the bsseq read.bismark command to read a genome wide cytosine report generated by bismark.
bsseq
updated 8 months ago by ▴ 740 • written 9 months ago by ▴ 20
6
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6
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2.7k
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WGCNA coupled with differential expression analysis: question about baseline module detection
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6
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11
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With DESeq2 "Not full rank" Error with design ~ line + time + condition
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updated 9 months ago by • 0 • written 9.3 years ago by ▴ 40
6
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10
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overlapsAny for elements in GRangesList
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updated 4 weeks ago by • 0 • written 8.0 years ago by ▴ 180
6
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7
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795
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Adding a group of samples reduces DEGs in other groups
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updated 9 months ago by 50k • written 9 months ago by ▴ 10
6
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BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
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9
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859
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biomaRt has encountered an unknown server error.
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updated 3 months ago by • 0 • written 3 months ago by • 0
6
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10
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1.7k
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Which input file is used for DGEList in EgdeR?
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updated 28 days ago by • 0 • written 15 months ago by ▴ 10
5
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2
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791
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ComBat_seq function in sva package does not return a matrix
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7 months ago Federico ▴ 10
5
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1
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464
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News: Bioconductor 3.18 is Released!
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written 6 months ago by 3.9k
5
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5
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2.0k
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Archive location for Bioconductor packages
archive
updated 9 months ago by 3.9k • written 21 months ago by ▴ 20
5
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3
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735
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 7 weeks ago by 50k • written 8 weeks ago by ▴ 50
5
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5
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825
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limma output for epic array methylation data
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9 months ago Jitendra ▴ 10
5
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7
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10k
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threshold to filter lowly expressed genes
edger rnaseq
updated 4 months ago by • 0 • written 7.2 years ago by • 0
5
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6
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669
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DataFrame Construction With Non-standard Column
S4Vectors
updated 7 months ago by 16k • written 7 months ago by ★ 1.5k
5
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6
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Differential protein/biomarker expression using limma: is that possible?
Proteomics NPX limma
updated 3 months ago by • 0 • written 3.2 years ago by ▴ 10
5
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7
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484
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DEG Filtering
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updated 7 weeks ago by 50k • written 8 weeks ago by • 0
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Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.2 years ago by ▴ 40
5
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1
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Support for new Illumina human methylation EPIC array v2
human methylationArrayAnalysis
updated 4 months ago by • 0 • written 14 months ago by ▴ 70
5
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2
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693
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outdated GEOmetadb.sqlite
GEOmetadb
15 months ago • updated 3 months ago Robert Castelo ★ 3.3k
5
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8
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Can the limma package be applied to Log2 RUV-normalized data?
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updated 5 months ago by • 0 • written 12 months ago by ▴ 10
5
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7
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1.1k
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different number of DEG because of outliers
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updated 4 months ago by 50k • written 14 months ago by • 0
5
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3
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721
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limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom blocking limma
updated 7 months ago by 50k • written 7 months ago by ▴ 180
5
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4
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Getting rs ids using chr coordinates | Biomart
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updated 10 months ago by 65k • written 3.8 years ago by • 0
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6
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Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 15 days ago by 65k • written 2.3 years ago by • 0
5
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6
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1.9k
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Questions about using training sets and WGCNA module eigengenes generated separately for Pigengene package
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6 months ago • updated 5 months ago kjngo ▴ 40
5
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4
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429
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Confusion about LFC using contrasts weights in EdgeR
edgeR
3 months ago • updated 12 weeks ago pl23 • 0
5
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2
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915
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can't install DESeq2 ("unable to access index for repository")
biocmanager DESeq2
9 months ago Alessia ▴ 40
5
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15
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Cross-species RNA-seq with DESeq2
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updated 11 months ago by 65k • written 6.9 years ago by ▴ 10
5
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9
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Batch correction and repeated measures
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updated 4 weeks ago by 50k • written 7 months ago by ▴ 10
5
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18
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Install DESeq2 problem for macbook pro M1 Max
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updated 4 months ago by • 0 • written 2.3 years ago by • 0
5
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3
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Cannot download GEOmetadb sqlite file
GEOmetadb
updated 3 months ago by • 0 • written 6.5 years ago by ▴ 10
5
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6
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877
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ASpli checks fail on Linux due to missing dependency to statmod
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updated 9 months ago by 50k • written 9 months ago by ▴ 10
5
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11
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Visualization of negative log CPM values
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5
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2
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Filter genes by expression for voomLmFit
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updated 5 months ago by 50k • written 5 months ago by • 0
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11
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How to annotate gene names for genomic coordinates?
annotation
written 8.9 years ago by • 0
5
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9
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974
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Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 29 days ago Chris ▴ 10
5
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6
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456
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 5 weeks ago by ★ 4.1k • written 5 weeks ago by ▴ 30
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25
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986
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limma models out of memory issue on Slurm HPC
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updated 6 weeks ago by 50k • written 7 weeks ago by ▴ 10
5
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7
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Question about setting threshold using filtering by expression on genes in edgeR
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updated 11 months ago by 50k • written 11 months ago by ▴ 10
5
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2
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701
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PhD student
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10 months ago Nisha • 0
5
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19
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6.0k
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DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 9 months ago by • 0 • written 2.8 years ago by ▴ 10
5
votes
6
replies
597
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
5
votes
9
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2.5k
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edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger calcnormfactors
updated 8 months ago by • 0 • written 6.5 years ago by ▴ 10
5
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8
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Limma design with continuous and categorical covariates
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updated 24 days ago by • 0 • written 7.8 years ago by ▴ 30
5
votes
5
replies
468
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create COMPOUND dataset (2 matrices) with rhdf5?
rhdf5
3 months ago baptiste ▴ 20
5
votes
3
replies
304
views
Log-cpm values from limma
limma edgeR RNASeq
updated 8 days ago by 50k • written 4 weeks ago by • 0
4
votes
7
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2.1k
views
should statmod be a dependency of limma and not a suggests?
limma
updated 9 months ago by 50k • written 8.0 years ago by • 0
4
votes
4
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1.1k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2 Dese DifferentialRegulation differe
updated 9 weeks ago by • 0 • written 13 months ago by ▴ 10
1,738 results • Page 2 of 35
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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