The Wayback Machine - https://web.archive.org/web/20230929060654/https://support.bioconductor.org/
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Do you like to drive or not?
NewWave
1 hour ago aletheabrown051 • 0
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25
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using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
6 hours ago Gregory • 0
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21
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Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
8 hours ago Luke • 0
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52
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DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 11 hours ago by 63k • written 12 hours ago by • 0
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67
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biomaRt code/getBM function no longer importing 'coding' sequence via seqType argument, "Invalid attribute(s): coding" error
biomaRt
updated 14 hours ago by ★ 6.1k • written 1 day ago by • 0
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52
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ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
19 hours ago • updated 17 hours ago Federico ▴ 10
0
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113
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error running exp2grn
NewWave
updated 18 hours ago by ▴ 40 • written 4 weeks ago by • 0
0
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45
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Singlecell protein surface (ADT) pseudotime techniques
monocle slingshot
20 hours ago EspressoKris ▴ 10
0
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2
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49
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shinyMethyl - saving the file
shinyMethyl
22 hours ago • updated 13 hours ago dorota.komar • 0
2
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4
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117
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Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
1 day ago • updated 7 hours ago Shihui • 0
0
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72
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Suggested package missing from Development version of Bioconductor
Devel
1 day ago • updated 21 hours ago Richard • 0
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mixOmics with Bioconductor classes
mixOmics
1 day ago Lluís Revilla Sancho ▴ 720
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featureCounts error Assertion failed: (NULL == pairer -> bam_margin_table -> appendix2), function SAM_pairer_finish_margin_table, file input-files.c,…
NewWave
1 day ago Kilian • 0
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73
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Batch effect adjust in model matrix
BatchEffect edgeR
updated 1 day ago by ★ 3.4k • written 1 day ago by • 0
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29
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HTSeqGenie runs very slow
HTSeqGenie
2 days ago zh9118 • 0
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
2 days ago franciscrick41 • 0
5
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223
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Batch correction and repeated measures
RUVSeq sva limma
updated 2 days ago by 48k • written 2 days ago by ▴ 10
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121
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DESeq2, results(dds, name = <reference>) interpretation results
DESeq2
2 days ago Rockbar • 0
0
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2
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108
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For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor clusterProfiler
updated 2 days ago by 63k • written 2 days ago by • 0
0
votes
1
reply
62
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Create design matrix for differential methylation analysis
Annotation annotate DifferentialMethylation minfiDataEPIC
updated 2 days ago by ▴ 720 • written 3 days ago by • 0
0
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1
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42
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Specifying evidence channels in STRINGdb
STRINGdb stringdb
3 days ago robynne.braun • 0
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32
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Variant Filtering on very large VCF files
VariantAnnotation VariantFiltering
3 days ago Bogdan ▴ 660
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165
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Deseq2, multifactor model design for comparing adult Mutant mouse versus pup Mutant mouse with normalization to the age difference of the Wildtype co…
DGE DESeq2
3 days ago ruba-mahmoud • 0
2
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93
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Remove duplicates of colData in TreeSummarizedExperiment
dplyr TreeSummarizedExperiment
updated 3 days ago by 40k • written 3 days ago by • 0
0
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5
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138
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DeSeq2 design fails (full model matrix is less than full rank)
DESeq2
updated 2 days ago by 63k • written 3 days ago by • 0
0
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2
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74
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Adding chromosome numbers to the respective gene ids of DESeq2 output file
NewWave hgu133a2.db
updated 3 days ago by ★ 3.4k • written 3 days ago by • 0
2
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6
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193
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DataFrame Construction With Non-standard Column
S4Vectors
updated 3 days ago by 16k • written 4 days ago by ★ 1.5k
0
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41
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Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
4 days ago kthapa • 0
0
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1
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103
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''Model_Matrix'' error
DifferentialExpression limma
updated 4 days ago by 48k • written 5 days ago by • 0
0
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2.9k
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Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 3.2 years ago by ▴ 80
1
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3
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1.3k
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How does DESeq2 calculate FPKM values when gene lengths are not supplied?
deseq2
written 3.5 years ago by • 0
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2.9k
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SRAdb: Error downloading sqlite files
sradb
written 5.9 years ago by • 0
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518
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blockwiseModule crashes in the end and doesn't generate modules
WGCNA
updated 2 hours ago by • 0 • written 5 months ago by • 0
2
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981
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Matching Variants Between Two VCF Objects
VariantAnnotation
written 2.8 years ago by ★ 1.5k
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4
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1.5k
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how to save subsetted GDS file
gwastools
written 5.4 years ago by ▴ 30
0
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1
reply
10k
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heatmap.2 - change column & row locations; angle / rotate
Cancer Cancer
written 9.9 years ago by ▴ 10
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2
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726
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Rgraphviz installation: DLL problem?
Rgraphviz Rgraphviz
written 13.7 years ago by ▴ 10
1
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6
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2.2k
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Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma edger timecourse without replicate voom
written 6.9 years ago by ▴ 10
1
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0
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46
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News: Bioconductor 3.18 db0s, OrgDbs, and TxDbs now available
db0 release Annotation
6 days ago kayla.interdonato 150
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0
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111
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Huge effect of a single sample on DEGs
limma
6 days ago • updated 11 hours ago Jonathan ▴ 10
0
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4
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183
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filtering out lowly expressed genes by groups
RNASeqData DESeq2
updated 6 days ago by 63k • written 7 days ago by ▴ 10
0
votes
1
reply
86
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Why dbConnect GEOmetadb_demo.sqlite shows some information while dbConnect GEOmetadb.sqlite shows no information
GEOmetadb GEOmetadb.sqlite dbConnect
updated 6 days ago by 63k • written 6 days ago by • 0
3
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4
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179
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DMRcate design
Epigenetics EpigeneticsWorkflow DMRcate
6 days ago • updated 2 days ago Jitendra ▴ 10
1
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1
reply
79
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Further analysis after limma regression output
statistics Epigenetics limma
updated 6 days ago by 63k • written 7 days ago by ▴ 10
1
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6
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358
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DelayedArray::read_sparse_block
DelayedArray
updated 5 days ago by 16k • written 5 weeks ago by ▴ 10
1
vote
2
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112
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Manual creation of qPCRset does not work
bug nondetects HTqPCR
7 days ago Ed Siefker ▴ 230
0
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3
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133
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ukb Chromosomal position information was converted into SNPS
SNPediaR
updated 7 days ago by 63k • written 8 days ago by • 0
1
vote
1
reply
85
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Deseq2, enrichGO and ensembl ID
go DESeq2
updated 7 days ago by 63k • written 8 days ago by • 0
1
vote
4
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161
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MDS plot edgeR
edgeR
updated 7 days ago by 48k • written 8 days ago by ▴ 10
0
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10
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246
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ensembldb::getGenomeTwoBitFile() not working for many species
AnnotationHubSoftware ensembldb
updated 8 days ago by 63k • written 8 days ago by • 0
44,790 results • Page 1 of 896
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Comment: blockwiseModule crashes in the end and doesn't generate modules by aletheabrown051 • 0
Re: [drift boss][1] Have you fixed this problem yet? [1]: https://driftboss.io
Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Shihui • 0
It makes sense that DeSeq2 normalized FPMs are more accurate. Thank you for the information!
Answer: DiffBind - how to prep the sample matrix when multiple bam files are used by MAC by James W. MacDonald 63k
If you essentially combined multiple BAM files in the MACS call, you could then just combine them using `samtools cat`, in which case you o…
Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Michael Love 40k
I can rephrase your question as: Why is number of reads not the superior estimate for the scaling factor (the "m" in rpm). There are som…
Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Shihui • 0
Hi Michael, Yes I manually calculated the RPMs by dividing each genes RPM to the library read depth. I didn't do any other normalization …
Votes
Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
Batch correction and Deseq2
A: Read counts between QSEA and MEDIPs
ComBat_seq function in sva package does not return a matrix
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