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2
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1.3k
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
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20 months ago mohammedtoufiq91 ▴ 10
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3
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1.3k
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recount3 problem downloading data from source sra
recount3
updated 20 months ago by ★ 1.1k • written 20 months ago by ▴ 10
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Running ENmix with mouse methylation manifest: readidat error - Error in readmanifest(manifestfile) : length(control.line) == 1 && is.integer(cont…
ENmix Bioconductor
updated 20 months ago by • 0 • written 20 months ago by ▴ 10
1
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1
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786
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Documenting resources in an `ExperimentHub` package?
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updated 20 months ago by 68k • written 20 months ago by • 0
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429
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Conditional analysis
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20 months ago SuperDad • 0
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1.1k
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FindOverlaps, makeVennDiagram and "others"
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20 months ago Raghad • 0
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2
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Errors in chromosome annotation-biomaRt
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20 months ago landenshanie ▴ 40
2
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10
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How to run allelic imbalance in apeglm
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20 months ago • updated 19 months ago euge.eugenio ▴ 20
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ERROR; return code from pthread_create() is 22
affy
updated 20 months ago by 68k • written 20 months ago by • 0
1
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3
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LRT, more than two conditions and pairwise comparisons
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updated 20 months ago by 68k • written 20 months ago by ▴ 740
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684
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Job: Post-Doc: Development of a new method to study the distribution of the effect sizes of QTL
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20 months ago pierre.devillemereuil • 0
1
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2
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876
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Subsetting RNAseq data | voomaByGroup()
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20 months ago Anna • 0
0
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0
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12
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Spam: Understanding Laser Hair Removal?
healthyControlsPresenceChecker
20 months ago shahrozimmac 0
0
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0
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540
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Processing of curatedmetagenomics
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20 months ago Edward • 0
7
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6
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Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
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written 21 months ago by • 0
0
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5
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all variables in design formula must be columns in colData (Deseq2) error
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20 months ago Galina • 0
0
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0
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699
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
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20 months ago Bibi • 0
0
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6
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Numerical differences in DESeq2 output depending on different design matrix construction
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20 months ago Ken C • 0
2
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4
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DESeq2- Mysterious interaction suppresses DEGs
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updated 20 months ago by 43k • written 20 months ago by • 0
0
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628
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Minor allele data from grch38 giving NAs from getBM ?
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20 months ago Abiologist • 0
0
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3
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1.6k
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STRINGdb : error with string_db$plot_network()
STRINGdb
updated 20 months ago by ▴ 110 • written 20 months ago by • 0
0
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2
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852
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DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
20 months ago makala • 0
2
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2
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Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
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20 months ago Matthew Thornton ▴ 390
0
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0
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determine k during RUVSeq
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20 months ago Ειρήνη • 0
2
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3
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Problem installing ChAMP on a MacBook
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updated 20 months ago by 4.3k • written 20 months ago by • 0
0
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794
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ReactomeGSA for RNASeq
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0
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Spam: Unveiling Unmatched Best Custom Patches
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20 months ago oliverelijhan 0
0
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0
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ChIPseeker peak_Profile_Heatmap color palette
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20 months ago Anton01 • 0
0
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GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
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20 months ago danalvoronov ▴ 10
0
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0
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query regarding how to apply WGCNA on replicates
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20 months ago k200987 • 0
3
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5
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Error while installing BiocManager::install("org.Vdahliae.eg.db")
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20 months ago Patadù ▴ 20
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4
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error running enricher from clusterprofiler
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20 months ago Yael • 0
3
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3
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How to correctly adjust for gender in edgeR
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updated 20 months ago by 53k • written 20 months ago by • 0
2
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How to design DEXSeq formula for multiple variables
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20 months ago • updated 19 months ago Sara • 0
4
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9
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Can DESeq2 rlog normalized matrix reflects time course result directly?
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updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
0
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0
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568
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Difference in Contrast in DiffBind
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20 months ago user_bioinfo • 0
1
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2
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Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
20 months ago Patadù ▴ 20
10
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11
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SGSeq: moving toward diffex from SGSeq analysis
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updated 20 months ago by • 0 • written 8.4 years ago by ▴ 80
0
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846
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Assymetric MA plot with no overall trend
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updated 20 months ago by 43k • written 20 months ago by • 0
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Batch effect correction: methylome data
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updated 20 months ago by ▴ 20 • written 20 months ago by • 0
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930
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News: Last Call: Nominations for Bioconductor Awards 2024! Deadline May 15
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22 months ago • updated 20 months ago shepherl 4.3k
1
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2
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Can log2cpm be used for proteomics data normalization?
metaMSdata
20 months ago Daniel • 0
0
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1
reply
845
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normalization across different species for DESeq2 analysis
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updated 20 months ago by 43k • written 20 months ago by • 0
1
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0
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News: Ensembl 112 has been released.
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20 months ago Aleena_Ensembl ▴ 30
1
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2
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QSEA- Extraction of Normalized methylation across the samples
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written 20 months ago by ▴ 10
0
votes
9
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2.5k
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
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updated 20 months ago by ▴ 70 • written 20 months ago by • 0
1
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3
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1.2k
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 20 months ago by 53k • written 20 months ago by • 0
3
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4
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1.0k
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Store output of matchPWM()
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21 months ago • updated 20 months ago mat149 ▴ 80
1
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2
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
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20 months ago BioinfGuru ▴ 70
0
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2
replies
728
views
Problem finding certain variables when importing a public database GSE73103
GSEABase GenomicDistributionsData
20 months ago Yveto • 0
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Comment: msmsTests, inconsistent sign between lFC.Av and LogFC by Ben • 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis by James W. MacDonald 68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by varying.mastodon.isyn • 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Comment: Confirm that OpenStats will not be archived (pryr dependency) by Marina • 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error by ansley.r.burtch • 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Votes
A: DESeq2 - VST eliminates zero values
Comment: Normalise to a housekeeping gene in DESEq2
Comment: limpa analysis advice
C: AnnotationForge makeOrgPackage rsqlite_send_query error
Answer: Limpa Pipeline Order
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