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1
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16
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putting my own expression data in deseq2
DESeq2
updated 1 hour ago by ★ 4.1k • written 2 hours ago by • 0
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0
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20
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Timecourse RNASeq analysis
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4 hours ago Aurora • 0
0
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0
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15
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Version 3.15 S4Vectors packages are missing
S4Vectors
7 hours ago bounlu • 0
0
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0
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11
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How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
8 hours ago SSSJec • 0
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0
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23
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
15 hours ago Agung • 0
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0
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31
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Could we detect difference at pathway level but not significant different at gene level?
GSVA
21 hours ago • updated 19 hours ago Chris • 0
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0
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60
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One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools TCGA
5 days ago glaciya2018 • 0
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0
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58
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
5 days ago • updated 1 day ago Sara • 0
0
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0
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61
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Exon-exon Junction Analysis for Variable-length Exons
Rsubread
5 days ago Dario Strbenac ★ 1.5k
0
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8
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304
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 5 days ago by ★ 1.3k • written 6 days ago by • 0
0
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2
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200
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featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
7 days ago • updated 5 days ago shuwangxinze1996 • 0
1
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13
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350
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Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
8 days ago • updated 5 days ago fernanda.backsouza ▴ 10
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0
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67
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Unlocking Potential: NURS FPX Strategies and Insights
levi NURSFPX ragene20sttranscriptcluster.db ssrch
9 days ago vaxahey107 • 0
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0
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84
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I am trying to detect alternative splicing.
ASpli
9 days ago Sebashish • 0
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0
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105
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Warning while loading DEP package
DEP
updated 11 days ago by 3.8k • written 11 days ago by • 0
1
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2
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196
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significant difference of p-values with dream() after updating VariancePartition
variancePartition
12 days ago • updated 11 days ago Le • 0
1
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2
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138
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Error in champ.load(): The following specified files do not exist
ChAMP
12 days ago • updated 11 days ago Sherin • 0
0
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1
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87
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Input Question for deseq.r
RSeqAn
updated 11 days ago by ★ 4.1k • written 12 days ago by • 0
0
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4
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208
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
12 days ago • updated 10 days ago lonn • 0
0
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0
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69
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Enzyme Engineering
BioTIP
13 days ago bocchemistry • 0
0
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0
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83
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Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror IsoCorrectoR
13 days ago Maliha Tabassum • 0
0
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1
reply
108
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what is the sampleFiles
chipseq
updated 13 days ago by 65k • written 14 days ago by • 0
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0
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83
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Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
14 days ago Virangika • 0
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0
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62
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[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
14 days ago Henry ▴ 10
0
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1
reply
117
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Deseq2 Rlog transformation
DESeq2
updated 15 days ago by ★ 4.1k • written 16 days ago by • 0
2
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2
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156
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[DiffBind] Obtaining normalization factors
DiffBind
17 days ago • updated 14 days ago Henry ▴ 10
0
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3
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236
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A ComBat-seq issue: the covariates are confounded
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updated 11 days ago by ▴ 850 • written 18 days ago by • 0
0
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0
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Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
18 days ago Stevie Pederson • 0
3
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6
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254
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Surrogate variable analysis for paired RNA seq experiment
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19 days ago • updated 18 days ago nhaus ▴ 30
0
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1
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162
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DESeq2 gives an error and R crashes
DESeq2
19 days ago • updated 18 days ago Shefali • 0
0
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0
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120
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LearnTaxa with custom Silva
DECIPHER LearnTaxa
19 days ago Eryn • 0
0
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0
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79
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queryDGIdb lexical error for some genes
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19 days ago Dennis • 0
0
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1
reply
143
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compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 15 days ago by ★ 3.9k • written 19 days ago by • 0
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0
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99
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ggtree tip label position (depth)
ggtree
20 days ago Roope • 0
2
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6
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369
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How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
21 days ago Chris • 0
0
votes
0
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136
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Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
24 days ago andromeda • 0
0
votes
1
reply
120
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Granges regionCounts not returning the expected number of entries
methylKit
25 days ago • updated 24 days ago Modoc Kesner ▴ 10
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0
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92
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flowDensity on a flowset
flowDensity
25 days ago fredrikwallberg • 0
0
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0
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81
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DMRcate error need at least two non-NA values to interpolate
DNAMethylation DMRcate
26 days ago Macsue • 0
0
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1
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147
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No output from read.bismark with bismark cov.files
bsseq methylation
updated 27 days ago by 65k • written 29 days ago by • 0
0
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2
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281
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Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR CopyhelpeR
29 days ago • updated 24 days ago fer_talavera • 0
0
votes
2
replies
243
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
29 days ago • updated 10 days ago isaac.vock • 0
0
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7
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363
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Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages Proxy Bioconductor GEOquery Internet_connection_problem
4 weeks ago • updated 27 days ago needNGS • 0
0
votes
1
reply
331
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Gene names from Matrix
BioCor StarBioTrek MatrixGenerics
updated 19 days ago by ▴ 730 • written 6 months ago by • 0
1
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7
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1.7k
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Error using champ.import
ChAMP EPICv2
updated 12 days ago by • 0 • written 10 months ago by • 0
1
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3
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833
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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 6 days ago by ★ 1.2k • written 14 months ago by ▴ 10
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1
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501
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Cibersort phenotype file
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updated 21 days ago by • 0 • written 15 months ago by • 0
0
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1
reply
544
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CopywriteR output
CopywriteR
updated 24 days ago by • 0 • written 2.5 years ago by • 0
48 results • Page 1 of 1
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Comment: putting my own expression data in deseq2 by ATpoint ★ 4.1k
> directly from GEOquery I can tell you that GEOquery retrieves array data not appropriate for DESeq2. For anything else make your questi…
Comment: Assist me in determining whether the analysis process using the limma package ha by SSSJec • 0
Thanks for your reply. I understand the principle of adjusted P-values, but I still want to address that issue. The description of the G…
Comment: Why p value inconsistent when using different number of pathway score? by Gordon Smyth 50k
Just a note that fgsea is not classical GSEA. The classical GSEA as described in the Subramanian paper and other papers from the Broad Inst…
Comment: Perform gene set enrichment analysis using fgsea on two conditions that don't ha by Chris • 0
Thank you! The resource I use may mispresent the requirement input of fgsea.
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha by alserg ▴ 260
fgsea doesn't require the presence of deferentially expressed genes, it takes as the input the differential expression-based ranking of all…
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Answer: Improving the design matrices vignette in RNAseq123
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Comment: DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
Comment: Why p value inconsistent when using different number of pathway score?
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