0
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1
reply
62
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compute_fasta_digest does not match Salmon index hash
tximeta
updated 2 hours ago by 43k • written 8 days ago by • 0
0
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0
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9
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News: Epigenomics data analysis with R and Bioconductor
chipseq MNaseSeq ATACSeq
4 hours ago info ▴ 10
1
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2
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128
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Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
annotation geneIDs flatheadmullet
updated 9 hours ago by 68k • written 12 hours ago by • 0
0
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1
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392
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News: List of Deprecated Packages for Bioc3.20
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5 months ago • updated 11 hours ago shepherl 4.1k
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1
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Issue with Soft-Thresholding in WGCNA
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updated 1 hour ago by • 0 • written 17 hours ago by • 0
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0
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17
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org.Sc.sgd.db
1 day ago irenejoshi07 0
1
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2
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Help with the code for "BiocNeighbors::generic_find_knn() function used by scran::quickCluster()
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4 days ago • updated 3 days ago Arctic • 0
0
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1
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489
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DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 4 days ago by ★ 4.8k • written 5 days ago by • 0
0
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1
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483
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Mismatch between Illumina Mouse Methylation BeadChip annotation and genome browsers (UCSC/Ensembl)
methylationArrayAnalysis MethylationArrayData
updated 5 days ago by 68k • written 5 days ago by • 0
1
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4
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Package developing and interoperation with Bioconductor
Package Bioconductor
6 days ago • updated 5 days ago slizchap • 0
4
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6
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Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 5 days ago by ★ 4.8k • written 28 days ago by • 0
0
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4
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Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
tximport rhdf5
6 days ago • updated 1 day ago Sofia • 0
1
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1
reply
714
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ComBat with repeated measures
ComBat sva
updated 5 days ago by ★ 4.8k • written 6 days ago by • 0
0
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0
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36
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News: List of Deprecated Packages for Bioc3.21
devel Release release Devel
6 days ago shepherl 4.1k
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0
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38
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News: Bioconductor 3.21 Release Schedule Important Deadlines Approaching
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0
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Correlation threshold
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7 days ago user_bioinfo • 0
0
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0
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4
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Spam: Does Spirit give free refunds?
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7 days ago Haggu 10
0
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0
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28
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Spam: Can I change my BA flight to another date?
org.Sc.sgd.db MafDb.1Kgenomes.phase1.GRCh38 ncdfFlow
7 days ago Haggu 10
1
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0
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22
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Spam: What is the cheapest day to fly on American Airlines? {Ask_Expert}
cadd.v1.6.hg38 MafDb.1Kgenomes.phase1.GRCh38 ncdfFlow
7 days ago Haggu 10
0
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0
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41
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CAGEr gep2pep hcg110.db
7 days ago Haggu 10
0
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0
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8
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Spam: vjkftykdtyk
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7 days ago Haggu 10
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2
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Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 7 days ago by ★ 4.8k • written 8 days ago by • 0
0
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2
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382
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Merging EPICV1 and V2 betas
minfiDataEPIC minfi
updated 5 days ago by • 0 • written 8 days ago by • 0
0
votes
1
reply
164
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Error in cnetplot
enrichplot clusterProfiler
updated 8 days ago by ★ 4.1k • written 14 days ago by • 0
0
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3
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480
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getBM from biomaRt inconsistencies found with .gtf files across multiple species
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updated 7 days ago by ★ 6.6k • written 8 days ago by ▴ 20
2
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3
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631
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Explanation for ROAST results
CAMERA limma
updated 7 days ago by 52k • written 8 days ago by • 0
0
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0
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111
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How do I set up my DESeq analysis when I know a few vehicle control samples provide background effects we don't want to see in any of the subsequent …
DESeq2 RUVSeq
8 days ago Simran • 0
1
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1
reply
132
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Merging annotation with differential expression output
annotation RNASeqData
updated 8 days ago by 68k • written 8 days ago by • 0
0
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2
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345
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Annotation package for Manduca sexta
annotation Manducasexta AnnotationData
9 days ago • updated 7 days ago GA ▴ 10
0
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5
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9 days ago kagodwi2 • 0
0
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4
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357
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Ensembl site unresponsive via biomaRt
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0
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1
reply
145
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best way to grouping GSM belonging to different datasets (with different platforms) and compare differential gene expression
GEOquery
updated 9 days ago by 68k • written 12 days ago by • 0
1
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2
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1.1k
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13 days ago • updated 6 days ago Joshua Llano • 0
1
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4
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367
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13 days ago • updated 8 days ago Lennie • 0
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5
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15 days ago • updated 12 days ago Kent • 0
5
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3
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updated 14 days ago by 52k • written 15 days ago by ▴ 10
2
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10
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ChAMPdata ChAMP
updated 15 days ago by • 0 • written 23 months ago by • 0
0
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1
reply
185
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GAGE kegg.gsets() self-signed certificate error
gageData gage
15 days ago • updated 13 days ago Lucas • 0
0
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2
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246
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myvariant error
myvariant getVariants
updated 15 days ago by • 0 • written 4 weeks ago by • 0
0
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4
replies
461
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
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written 15 days ago by • 0
0
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0
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DiffBind multi-tissue comparison
DiffBind
16 days ago lryrainche • 0
1
vote
2
replies
391
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affy::rma results doesn't match with ncbi website
affy Preprocessing Microarray
updated 16 days ago by 68k • written 17 days ago by • 0
0
votes
4
replies
264
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Problem installing package TxDb.Mmusculus.UCSC.mm10.knownGene
TxDb.Mmusculus.UCSC.mm10.knownGene
16 days ago • updated 15 days ago Wolfgang RAFFELSBERGER ▴ 140
0
votes
0
replies
108
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
17 days ago GT • 0
1
vote
1
reply
771
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
updated 19 days ago by 68k • written 19 days ago by • 0
0
votes
2
replies
611
views
Clarification on GOALL / GO2ALLORFs mapping
org.Sc.sgd.db
20 days ago • updated 14 days ago DavideSant • 0
2
votes
2
replies
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Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
22 days ago • updated 16 days ago Elizabeth • 0
1
vote
2
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1.2k
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[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
22 days ago • updated 21 days ago Luca • 0
0
votes
1
reply
279
views
Discrepancy between Excel TPP-TR reported values and the Melt Curve reported values
TPP
updated 21 days ago by 68k • written 22 days ago by • 0
1
vote
3
replies
827
views
Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malformed error
signac AnnotationHub
written 23 days ago by ▴ 110
46,431 results • Page 1 of 929
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Comment: Phyloseq: How to add sample table to phyloseq object by chillykean • 0
@[Chill Guy Clicker][1]: You can add sample_table by creating a data frame containing sample information and using sample_data(myobject) <-…
Comment: Issue with Soft-Thresholding in WGCNA by dirty.cougar.risi • 0
Interesting data! Looking at these genes, it's like navigating a complex maze. The fluctuating values remind me of chasing high scores in […
Answer: compute_fasta_digest does not match Salmon index hash by Michael Love 43k
Can you provide more details on when this is happening? The salmon index is the definitive hash associated with the quant files, so I'm con…
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species by James W. MacDonald 68k
Oh wait. You want to map from Ensembl to NCBI? That's hard to do with model organisms, let alone non-model. This `OrgDb` doesn't have Ensem…
Answer: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species by James W. MacDonald 68k
You can use the `AnnotationHub` ``` > library(AnnotationHub) > hub <- AnnotationHub() |===========================| 100% sna…
Votes
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
what the test method for enrichGO in clusterProfiler?
A: single-cells RNA-seq analysis by MAST with unbalanced group size
Comment: plyranges: find exact GRanges match keeping metadata columns
Answer: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran
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