0
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1
reply
36
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How fix lines of dendrogram that overlap in the column portion of a heatmap?
heat heatmaps
updated 6 hours ago by 60k • written 22 hours ago by • 0
0
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10
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set.seed in function vs clusterSetRNGStream: switching from one to another
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6 hours ago ZheFrench ▴ 30
0
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14
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Compare different cell lines with tissues using limma
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7 hours ago Sam • 0
3
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2
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36
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FeaturePlot in scater
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9 hours ago • updated 5 hours ago Guandong Shang ▴ 20
0
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1
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48
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Analyzing barcode sequencing experiments with DESeq2/edgeR
edgeR DESeq2
updated 16 hours ago by 45k • written 21 hours ago by • 0
0
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3
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60
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How can i fix this problem in R
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updated 9 hours ago by ★ 1.3k • written 19 hours ago by • 0
0
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1
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32
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Use of Scater for QC in scRNA-seq: How to remove cells with less than certain number of genes supported with certain number of reads
SingleCellExperiment
updated 23 hours ago by ★ 1.3k • written 1 day ago by • 0
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18
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Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
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1 day ago Palmira • 0
0
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1
reply
31
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What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
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updated 1 day ago by ★ 3.3k • written 1 day ago by • 0
0
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1
reply
39
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What are the data values in qRT-PCR for statistical testing? dCT? or 2^-dCT?
qRT-PCR CTvalue
updated 1 day ago by 60k • written 1 day ago by • 0
0
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1
reply
53
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Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
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updated 1 day ago by ★ 1.3k • written 1 day ago by • 0
9
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9
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196
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Using Age or other numerical variable to model expression in deseq2
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updated 6 hours ago by 60k • written 2 days ago by • 0
0
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46
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Error with TCGA package - TCGAbiolinks
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2 days ago JAcky • 0
0
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1
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61
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Bioconducter can not be installed on latest RStudio
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updated 2 days ago by ★ 5.6k • written 2 days ago by • 0
0
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1
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53
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Using queryMany() in mygene package: Problem of querying Entrez gene IDs based on UniGene IDs in rat.
mygene queryMany
updated 2 days ago by ★ 3.3k • written 5 days ago by • 0
0
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1
reply
67
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GC content
EDASeq
updated 2 days ago by ★ 1.3k • written 4 days ago by • 0
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0
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28
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Timeout error when querying DGIDB
rDGIdb
2 days ago Jannah • 0
0
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4
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120
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I got error message about DESeqDataSetFromMatrix
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updated 2 days ago by ★ 1.1k • written 3 days ago by • 0
2
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6
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479
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DESeq2: relevel() unsuccessfully setting control group
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updated 3 days ago by • 0 • written 15 months ago by ▴ 10
1
vote
3
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231
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miRNA differential expression analysis - treat as transcript level?
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updated 3 days ago by 37k • written 9 days ago by • 0
0
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0
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51
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Differential expression with single cell data: any good two component (hurdle) models recently?
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5 days ago • updated 4 days ago Nik Tuzov ▴ 70
3
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9
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220
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Help with limma contrast, difference of a difference?
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5 days ago • updated 4 days ago Ahdee ▴ 50
0
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6
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124
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How to change all text, including point labels to Arial?
EnhancedVolcano
updated 5 days ago by 60k • written 6 days ago by • 0
0
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DiffBind: GreyListChIP error: Error: $ operator is invalid for atomic vectors
DiffBind
5 days ago millerh1 • 0
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2
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74
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Scaling for p.heatmap
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5 days ago • updated 1 day ago Bhavana • 0
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4
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Confused about using RUVg in getting negative control genes using RUVg
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9 days ago • updated 2 days ago Mohamed • 0
0
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3
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91
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I got error when visualizing my PCA
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updated 5 days ago by ▴ 140 • written 5 days ago by • 0
0
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0
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42
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Is there a Bioconductor package to calculate TFs regulatory networks?
TFs Transcription regulator
5 days ago OliverBoynton • 0
1
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3
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86
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Trouble importing my own Gene Ontology Annotation into topGO
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updated 2 days ago by 60k • written 6 days ago by ▴ 60
1
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6
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130
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RSEM - tximport; where is effective_length information used? Implications for scRNA?
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6 days ago • updated 3 hours ago Kelen • 0
0
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0
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31
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Typo in citation for RNASeqPower
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6 days ago stephenjjohnson • 0
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0
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diffbind dba.report
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6 days ago jonathanho1989 • 0
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8
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220
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Finding differentially expressed genes in a prospective cohort study
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7 days ago • updated 2 days ago YC • 0
1
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4
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How to create an aldex.clr object from a "selex" data table
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7 days ago • updated 6 days ago Greg • 0
3
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5
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150
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Pathview unable to download pathways
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updated 7 days ago by 3.1k • written 8 days ago by ▴ 10
0
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3
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106
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Problem in kegga() and others getting data from KEGG after switch from http to https
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updated 7 days ago by 3.1k • written 7 days ago by ★ 2.0k
0
votes
1
reply
65
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extendedSequences length is not the required for DeepCpf1 (34bp)
CRISPRseek
9 days ago • updated 7 days ago Miguel • 0
1
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2
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98
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ENSEMBL to ENTREZ ID
clusterProfiler
7 days ago martacrespi7 • 0
0
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2
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95
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Error in NxtIRFcore
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7 days ago ieki.tky • 0
2
votes
3
replies
96
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Large difference between lfcshrink and non-shrunk DESeq2 results
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7 days ago Dave • 0
0
votes
2
replies
87
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Get confused about the mean log-intensity (Amean)
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8 days ago • updated 7 days ago OE • 0
1
vote
5
replies
118
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Unable to load mm10 genome for use with GenomicDistributions package
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8 days ago • updated 7 days ago rashford • 0
0
votes
1
reply
72
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Pathview error Warning: Parsing ./mmu04928.xml file failed, please check the file!
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updated 8 days ago by ★ 3.3k • written 21 days ago by • 0
0
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0
replies
44
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Diffbind analysis of ATAC-seq data
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8 days ago • updated 7 days ago young • 0
2
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2
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Can't load UCSC transcript IDs
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updated 8 days ago by ★ 3.3k • written 8 days ago by • 0
3
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1
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111
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RFC: Inconsistent software license for scran & automated license checks
agpl license gpl scran
updated 8 days ago by 6.6k • written 15 days ago by ▴ 30
0
votes
20
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465
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Different DESeq2 results (both FC and pvalue) by changing col/row orders in input
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9 days ago • updated 7 days ago Weisheng • 0
1
vote
2
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107
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deseq2 lfc shrinkage with few DEGs
RNASeq DESeq2
9 days ago Victor • 0
0
votes
3
replies
112
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Persisting error in making a heatmap
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10 days ago • updated 7 days ago beslinail • 0
3
votes
3
replies
134
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Nested analysis or Collapsed-replicate analysis?
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updated 9 days ago by 37k • written 19 days ago by • 0
42,716 results • Page 1 of 855
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Replies
Comment: why org.Hs.egGO2ALLEGS contain genes number difference from GO database? by pengmin.wang.1 • 0
yes, I also find genes in org.Bt.egGO2ALLEGS (bovine) are always less than online GO database in the same term. So do you know how to get t…
Comment: how to get gene list for given GO terms? by pengmin.wang.1 • 0
Hi, do you know how to get the gene list that have annotations from online GO database. For example, y <- as.list(org.Bt.egGO2ALLEGS), y co…
Comment: RSEM - tximport; where is effective_length information used? Implications for sc by Kelen • 0
Thank you. Gene-level analysis. I don't yet have a specific downstream pipeline in mind - I am trying to understand what limitations I migh…
Comment: FeaturePlot in scater by Guandong Shang ▴ 20
Thanks, this is what I want!
Comment: Using Age or other numerical variable to model expression in deseq2 by James W. MacDonald 60k
If you converted to a factor, the intercept is the reference level (you have to look at `levels(age)` to know what the reference is). If yo…
Votes
A: paired and unpaired test at the same time with voom limma
Comment: Duplicate correlation with limma in before-after exposure experiment
Answer: Using Age or other numerical variable to model expression in deseq2
Comment: Using Age or other numerical variable to model expression in deseq2
Comment: Using Age or other numerical variable to model expression in deseq2
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