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6
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Deseq2 and Normalization of RNA sequencing data
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1 hour ago kcarey • 0
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Differences in differential analysis methods for RNA-Seq
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Empty table plot using plotGseaTable()
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5 hours ago • updated 3 hours ago Chris • 0
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Could we detect difference at pathway level but not significant different at gene level?
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2 days ago Chris • 0
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72
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One error problem occurred caused by data type during using GDCprepare to handle BRCA data
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6 days ago glaciya2018 • 0
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how to do Differential splicing from SGSeq analysis
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7 days ago • updated 2 days ago Sara • 0
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Exon-exon Junction Analysis for Variable-length Exons
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7 days ago Dario Strbenac ★ 1.5k
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DESeq2 output used for PCA plot on R studio
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updated 6 days ago by ★ 1.3k • written 8 days ago by • 0
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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
8 days ago • updated 6 days ago shuwangxinze1996 • 0
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13
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365
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Trying to use enrichGO
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10 days ago • updated 7 days ago fernanda.backsouza ▴ 10
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Unlocking Potential: NURS FPX Strategies and Insights
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10 days ago vaxahey107 • 0
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I am trying to detect alternative splicing.
ASpli
11 days ago Sebashish • 0
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0
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109
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Warning while loading DEP package
DEP
updated 13 days ago by 3.8k • written 13 days ago by • 0
1
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2
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204
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significant difference of p-values with dream() after updating VariancePartition
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13 days ago Le • 0
1
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2
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145
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Error in champ.load(): The following specified files do not exist
ChAMP
14 days ago • updated 13 days ago Sherin • 0
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92
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Input Question for deseq.r
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updated 13 days ago by ★ 4.1k • written 14 days ago by • 0
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4
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220
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Differential peaks that were not identified in diffbind were identified in diseq2
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14 days ago • updated 11 days ago lonn • 0
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Enzyme Engineering
BioTIP
14 days ago bocchemistry • 0
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0
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Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror IsoCorrectoR
15 days ago Maliha Tabassum • 0
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111
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what is the sampleFiles
chipseq
updated 15 days ago by 65k • written 15 days ago by • 0
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0
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Diffbind Error in socketConnection
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16 days ago Virangika • 0
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[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
16 days ago Henry ▴ 10
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1
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121
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Deseq2 Rlog transformation
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updated 16 days ago by ★ 4.1k • written 17 days ago by • 0
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[DiffBind] Obtaining normalization factors
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19 days ago • updated 15 days ago Henry ▴ 10
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3
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A ComBat-seq issue: the covariates are confounded
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updated 13 days ago by ▴ 850 • written 19 days ago by • 0
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Cannot use `readVcf()` on a file created with `writeVcf()`
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19 days ago Stevie Pederson • 0
3
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6
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Surrogate variable analysis for paired RNA seq experiment
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20 days ago nhaus ▴ 30
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170
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DESeq2 gives an error and R crashes
DESeq2
21 days ago • updated 20 days ago Shefali • 0
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0
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124
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LearnTaxa with custom Silva
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21 days ago Eryn • 0
0
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0
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queryDGIdb lexical error for some genes
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21 days ago Dennis • 0
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151
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compareCluster dotplot: how to modify the genesets order
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updated 17 days ago by ★ 3.9k • written 21 days ago by • 0
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104
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22 days ago • updated 21 days ago Roope • 0
2
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6
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379
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How to make boxplot with pairwise and overall p value from Limma
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23 days ago Chris • 0
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Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
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26 days ago andromeda • 0
0
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1
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123
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Granges regionCounts not returning the expected number of entries
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27 days ago • updated 26 days ago Modoc Kesner ▴ 10
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27 days ago fredrikwallberg • 0
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DMRcate error need at least two non-NA values to interpolate
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27 days ago Macsue • 0
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1
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154
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No output from read.bismark with bismark cov.files
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updated 29 days ago by 65k • written 4 weeks ago by • 0
0
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2
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286
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Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
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4 weeks ago • updated 26 days ago fer_talavera • 0
0
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2
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247
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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4 weeks ago • updated 12 days ago isaac.vock • 0
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7
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379
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Internet connection for Bioconductor packages in Rstudio in Iran...
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4 weeks ago • updated 29 days ago needNGS • 0
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How to extract the coordinate of dba.plotPCA?
DiffBind PCA
4 weeks ago feather-W • 0
0
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0
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105
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PCA plot for normalized counts using Diffbind
DiffBind PCAplot
4 weeks ago Ankit ▴ 20
1
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5
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327
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fgsea fork
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updated 4 weeks ago by 65k • written 4 weeks ago by • 0
0
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0
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92
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
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4 weeks ago Pierre Lindenbaum ▴ 10
3
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3
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382
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Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater runPCA
updated 5 weeks ago by ▴ 160 • written 5 weeks ago by • 0
0
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0
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114
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Using Granges to find overlapping pairs at exactly 10kb distance
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5 weeks ago gshweta95 • 0
2
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1
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203
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Only positive enrichment score in GSEA
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updated 5 weeks ago by ★ 3.9k • written 5 weeks ago by ▴ 10
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0
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112
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Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
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5 weeks ago nromerov • 0
1
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3
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256
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cBioPortalData loads empty z-score expression table
cBioPortalData
updated 5 weeks ago by 690 • written 5 weeks ago by • 0
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Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM() by James W. MacDonald 65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Votes
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
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