0
votes
0
replies
19
views
Error in UseMethod("rescale")
clusterProfiler
7 hours ago • updated 6 hours ago vvelagal • 0
1
vote
6
replies
75
views
KEGG enrichment analysis for non model organism
RNAseq123
13 hours ago • updated 11 hours ago afsanarupa1 • 0
1
vote
3
replies
47
views
Unable to load data from duffel.rail
recount recountWorkflow recount3
updated 5 hours ago by ▴ 1000 • written 16 hours ago by • 0
2
votes
3
replies
61
views
How to use a specific Bioconductor version in custom Dockerfile
singularity ensemblVEP docker
1 day ago • updated 9 hours ago jtaylor-predicine • 0
0
votes
0
replies
12
views
Error in loadFUN(x, seqname, ranges) : trying to load regions beyond the boundaries of non-circular sequence "chr2"
HiCDCPlus BSgenome.Hsapiens.UCSC.hg38
1 day ago Yue • 0
0
votes
1
reply
28
views
In readLines(csvfile)
pipeline testdata ChAMP
updated 1 day ago by 61k • written 1 day ago by • 0
0
votes
10
replies
110
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub AnnotationForge Pseudomonas_aeruginosa
1 day ago • updated 1 hour ago Manmohit • 0
0
votes
5
replies
79
views
Build custom TxDb Package using makeTxDbPackage
GenomicFeatures
updated 12 hours ago by 61k • written 1 day ago by • 0
0
votes
0
replies
25
views
GO.db GOGeneSets cannot be used with org.Sc.sgd.db . Any alternative?
GOGeneSets HTSanalyzeR2 GO.db org.Sc.sgd.db yeast
1 day ago lululululucy • 0
0
votes
2
replies
56
views
abs() error in rstudio
Bioconductor BiocManager abs() Bioinformatics
written 5 days ago by • 0
0
votes
2
replies
43
views
Does the knock down cause transcriptome-wide differences in isoform usage for Pac-Bio data?
pacbio isoform
written 6 days ago by • 0
0
votes
0
replies
21
views
Correction for multiple comparison by DeSeq2 - treatment1 vs. control, treatment2 vs. control, ... treatment n vs. control
DESeq2 MultipleComparison r
1 day ago ncorak • 0
5
votes
6
replies
116
views
How to interpret Histogram of average log2 CPM filtering in EdgeR?
CPM filterByExpr edgeR histogram rowsums
1 day ago mohammedtoufiq91 ▴ 10
1
vote
3
replies
82
views
Limma-voom - Timepoint by timepoint comparison in timecourse experiment
limma
written 7 days ago by ▴ 20
0
votes
2
replies
50
views
could not find function "get_known_signatures"
MutationalPatterns
updated 1 day ago by 6.6k • written 2 days ago by ▴ 60
2
votes
1
reply
61
views
HMP1-II Metagenomic Data
MicrobiomeData curatedMetagenomicData
updated 2 days ago by 1.1k • written 6 days ago by ▴ 20
3
votes
2
replies
77
views
Rlog performed on tpm or raw transcript abundances?
DESeq2 rlog
written 3 days ago by • 0
0
votes
2
replies
67
views
Problem with multiple sequence alignment using AlignSeqs
R dada2 DECIPHER
3 days ago • updated 8 hours ago Nelli • 0
0
votes
2
replies
85
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
5 days ago • updated 1 day ago Lisa • 0
0
votes
2
replies
87
views
checkFullRank(modelMatrix) while neither factor can be predicted from each other.
DESeq2
updated 3 days ago by ★ 1.2k • written 3 days ago by • 0
1
vote
5
replies
169
views
Adding geneID to list of gene locus IDs
cluster OrgDb clusterProfiler
updated 3 days ago by 61k • written 20 days ago by • 0
0
votes
2
replies
64
views
Deseq2 , result() taking too long > 3hrs
DESeq2
3 days ago • updated 1 day ago Nidhi • 0
0
votes
0
replies
20
views
CoGAPS Installation Problem - clang compiler does not support '-march=native'
CoGAPS clang
3 days ago MayerAdam • 0
0
votes
1
reply
56
views
How to correctly interpret ALDEx2 output - differential abundance testing
MicrobiomeData ALDEx2
3 days ago • updated 1 day ago RvH • 0
1
vote
2
replies
84
views
Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
3 days ago mohammedtoufiq91 ▴ 10
0
votes
2
replies
73
views
CAGEr bug report: wrong consensus cluster results
CAGEr
6 days ago • updated 3 days ago Meng • 0
0
votes
1
reply
82
views
FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 4 days ago by ★ 1.2k • written 4 days ago by • 0
0
votes
0
replies
29
views
RUVg for SNAP-ChIP ?
RUVSeq
5 days ago Bogdan ▴ 660
0
votes
2
replies
120
views
Error when Installing BioConductor Package ('affy')
Bioconductor Install affy
updated 5 days ago by 6.6k • written 5 days ago by • 0
4
votes
8
replies
212
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 5 days ago by 46k • written 6 days ago by ▴ 10
1
vote
2
replies
64
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
6 days ago mohammedtoufiq91 ▴ 10
1
vote
9
replies
229
views
countToFPKM and featureLength
countToFPKM
updated 4 days ago by ★ 1.2k • written 6 days ago by • 0
0
votes
0
replies
48
views
RNA seq analysis
RNASeq
6 days ago lesseyl • 0
11
votes
17
replies
353
views
SV4Vectors DataFrame bug with haven_labelled data
S4Vectors DataFrame haven_labelled haven
updated 1 day ago by ▴ 20 • written 6 days ago by ▴ 20
1
vote
3
replies
67
views
DESeq2 on multiple sample groups
DESeq2
written 6 days ago by • 0
3
votes
7
replies
194
views
Is it possible to convert "DESeq2's normalized counts" to "DEGs"?
DESeq2 raw
updated 6 days ago by ★ 1.2k • written 13 days ago by • 0
0
votes
2
replies
73
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
6 days ago Konstantinos • 0
0
votes
2
replies
121
views
Setting up contrasts within a dataset within conditions (across different genotype) and across conditions (for the same genotype)
DESeq2
8 days ago • updated 3 days ago nrama • 0
0
votes
0
replies
53
views
EdgeR without replication
Transcriptomics
6 days ago kuttibiotech2009 • 0
0
votes
0
replies
29
views
Reducing dataset size to improve run time for fitGAM in tradeSeq
tradeSeq pseudotime
6 days ago fluentin44 • 0
0
votes
0
replies
25
views
HiCDCPlus `construct_features` incompatible with BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0 annotation
HiC-DC+ HiCDCPlus
6 days ago Yue • 0
0
votes
3
replies
129
views
Cannot download flowUtils package from Bioconductor 3.16
Bioconductor flowUtils
updated 6 days ago by ★ 5.8k • written 6 days ago by • 0
1
vote
2
replies
669
views
ReactomePA:enrichPathway error in universe parameter
enrichPathway ReactomePA
updated 6 days ago by ▴ 40 • written 2.6 years ago by ▴ 10
1
vote
1
reply
53
views
Problems installing methylumi package
methylumi
updated 7 days ago by ★ 5.8k • written 7 days ago by • 0
2
votes
3
replies
142
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
8 days ago • updated 6 days ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
51
views
TCGA RNAseq Normalization
normalization RNASEQ Normalization TCGAutils TCGA
updated 7 days ago by ★ 1.9k • written 7 days ago by • 0
0
votes
2
replies
76
views
ape::dnds produces nan value
R ape dnds nan nanotubes
7 days ago • updated 4 days ago Working • 0
0
votes
2
replies
76
views
Getting this error while trying to use edgeR "Error in as.vector(x, mode) : cannot coerce type 'closure' to vector of type 'any'"
edgeR edge
updated 7 days ago by 46k • written 8 days ago by • 0
0
votes
0
replies
53
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
7 days ago Konstantin • 0
2
votes
1
reply
96
views
How to interpret DESeq2's padj after setting lfcThreshold and the log2FC is greater than lfcThreshold?
DESeq2
updated 8 days ago by 38k • written 9 days ago by ▴ 10
43,497 results • Page 1 of 870
Recent ...
Replies
Comment: Question about contrasts in DESeq2 by marinaw ▴ 10
Thank you Michael!
Comment: Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and by Manmohit • 0
WHen I am trying to install the package using BiocManager::Install it gives me error ``` BiocManager::install("./org.Paeruginosa.eg.db", …
Comment: Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and by Manmohit • 0
Thanks James for suggestion. This worked
Comment: Unable to load data from duffel.rail by Leonardo Collado Torres ▴ 1000
One of the SciServer (file host) admins can likely resolve this issue but is traveling today. So you might want to wait 24 hrs before tryin…
Comment: Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and by James W. MacDonald 61k
You could download the file from expasy.org directly, put it in your working directory, and use rebuildCache = FALSE in your call to `makeO…
Votes
Answer: KEGG enrichment analysis for non model organism
Answer: How to use a specific Bioconductor version in custom Dockerfile
Answer: How to use a specific Bioconductor version in custom Dockerfile
Comment: Unable to load data from duffel.rail
A: DESeq2 contrast using list
Awards • All
Popular Question to Leonardo Collado Torres ▴ 1000
Scholar to Gordon Smyth 46k
Scholar to James W. MacDonald 61k
Popular Question to ZheFrench ▴ 40
Popular Question to lcordeiro • 0
Locations • All
United States, 2 minutes ago
Bangladesh, 2 minutes ago
San Diego, 52 minutes ago
Taiwan, 1 hour ago
United States, 1 hour ago
Traffic: 273 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6