0
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4
replies
953
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Limma multi-group, nested analysis with aggregation
limma
12 months ago • updated 9 months ago Jonathan ▴ 10
0
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0
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550
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what should be the input for SingleR() automatic cell type annotation?
SingleR
11 months ago Yijing • 0
0
votes
0
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145
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DEXSeq plot error
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9 weeks ago jean-christophe.helbling • 0
0
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0
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381
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[Rsamtools] pileup option max_depth behaviour
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10 months ago romain.lannes • 0
0
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0
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183
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Could SGSeq utilizes "ts" tag produced from minimap2 other than "XS" tag?
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11 weeks ago jk • 0
0
votes
0
replies
117
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flowDensity on a flowset
flowDensity
6 weeks ago fredrikwallberg • 0
0
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0
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179
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Comparing the effects of a condition over time in two seperate tissues
MAST
12 weeks ago Dillon • 0
1
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3
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1.9k
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enrichKEGG results for non-model organism
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updated 3 months ago by • 0 • written 23 months ago by • 0
0
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0
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76
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Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer ShinyApps
9 days ago neilzhao ▴ 30
1
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3
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1.6k
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regionCounts() from csaw - object 'fancy_mseq' not found
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updated 5 months ago by • 0 • written 2.0 years ago by • 0
0
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0
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154
views
Postdoc
TCGAWorkflow
3 months ago sameerahmadguru • 0
0
votes
3
replies
749
views
DECIPHER IdTaxa: Speed up training?
DECIPHER idtaxa
updated 10 months ago by ▴ 150 • written 10 months ago by ▴ 30
1
vote
2
replies
687
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Error running run_app('LFQ')
LFQ DEPpackage run_app('LFQ') ShinyApps DEP
updated 10 months ago by ▴ 210 • written 11 months ago by ▴ 10
0
votes
0
replies
365
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adding noise to scRNA Seq counts
scRNAseq
10 months ago Jiyuan • 0
0
votes
1
reply
288
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DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
4 months ago WS • 0
0
votes
1
reply
238
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"Counts" in enrichGO
GSEABase
updated 3 months ago by ▴ 10 • written 3 months ago by • 0
1
vote
1
reply
425
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 6 months ago by ▴ 190 • written 6 months ago by ▴ 10
0
votes
0
replies
175
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rpk per cell saved in SCE object.
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4 months ago JalapenoCornbread • 0
2
votes
6
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2.0k
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clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
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updated 4 months ago by ★ 4.0k • written 14 months ago by ▴ 10
0
votes
3
replies
496
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determine if R package or it's dependencies functionality require internet access
biomaRt
updated 6 months ago by 50k • written 6 months ago by • 0
0
votes
0
replies
250
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Can I plot values from LINCS level 4?
cmapR
11 months ago Alexandre • 0
1
vote
0
replies
492
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WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 11 months ago by 42k • written 11 months ago by ▴ 20
0
votes
1
reply
988
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How to get Cytogenetic band for muscles gene by using Biomart or other tools in R
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written 2.5 years ago by • 0
2
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1
reply
233
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Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 7 weeks ago by ★ 4.0k • written 8 weeks ago by ▴ 10
0
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0
replies
13
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Spam: What happens after 99999 in chrome dinosaur game?
Experimental
4 months ago larsenlola06 0
0
votes
0
replies
158
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Feature Counts -R XS Read Assignment Tag
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10 weeks ago chris2.a.white • 0
0
votes
0
replies
167
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Can I combine collinear variables into a single value
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11 weeks ago Harrsha • 0
0
votes
0
replies
343
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10 months ago sonal • 0
0
votes
0
replies
375
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Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
6 months ago mch • 0
0
votes
0
replies
300
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Dual species RNA-seq, Library size and normalization
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7 months ago Florian • 0
0
votes
2
replies
264
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TCGA-GBM subtype tumor
curatedTCGAData
updated 3 months ago by 700 • written 3 months ago by • 0
0
votes
3
replies
888
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How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.
clusterProfiler OrganismDb
updated 5 months ago by ★ 4.0k • written 5 months ago by • 0
0
votes
4
replies
325
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
11 weeks ago mperalc • 0
0
votes
0
replies
384
views
Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
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9 months ago Mohamed ▴ 30
0
votes
0
replies
105
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
5 weeks ago Stevie Pederson • 0
0
votes
3
replies
176
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ChAMP installation issue
Cha ChAMP
6 days ago • updated 5 days ago e1271094 • 0
0
votes
0
replies
99
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flowStats for CyTOF
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16 days ago tholmes • 0
0
votes
0
replies
267
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SomaticSignatures normalization for trinucleotide motifs in reference genome
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6 months ago vasily.dobrovolsky • 0
0
votes
0
replies
153
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lfcSE
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11 weeks ago Gordon • 0
0
votes
1
reply
255
views
Conversion of .sf to .rgel format for the salmon processed files with transcript to gene mapping.
RnaSeqSampleSize
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
0
votes
0
replies
183
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
4 months ago Aswathy • 0
0
votes
2
replies
460
views
DESeq2: how could the lower mean abundance treatment show a positive and significant LFC?
DESeq2
7 months ago • updated 6 months ago Roey Angel • 0
0
votes
0
replies
418
views
Title in dba.plotProfile
DiffBind
11 months ago agata17 • 0
0
votes
1
reply
521
views
Subsetting cells from a single cell experiment
SingleCellExperiment
written 7 months ago by • 0
0
votes
6
replies
856
views
Merge 2 accounts, or delete 1 account.
Bioconductor ALL
11 months ago simone.tiberi • 0
0
votes
2
replies
1.7k
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ChAMP pipeline error (champ.import)
software error
written 5.1 years ago by • 0
0
votes
0
replies
445
views
Help with error running DiffBind
DiffBind
11 months ago Chris ▴ 10
0
votes
0
replies
285
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Gene names not included on KEGGgraph plots
KEGGgraph
11 months ago hilarius_bookbinder • 0
0
votes
1
reply
611
views
DNABarcodes: issue with wrong barcode decoding
single-cell sequencing barcodes
updated 3 months ago by • 0 • written 5.1 years ago by ▴ 160
0
votes
1
reply
326
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HTSeqGenie runs very slow
HTSeqGenie
7 months ago zh9118 • 0
402 results • Page 2 of 9
Recent ...
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Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
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?
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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
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