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Votes
3
votes
3
replies
179
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
15 days ago • updated 10 days ago
jacques.imbert
• 0
3
votes
2
replies
178
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 5 days ago by
Guido Hooiveld
★ 3.9k • written 8 days ago by
fernanda.backsouza
▴ 10
0
votes
2
replies
177
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
25 days ago • updated 24 days ago
Gimena
• 0
2
votes
2
replies
176
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
15 days ago
julia_mcdonough
• 0
2
votes
5
replies
175
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 2 days ago by
James W. MacDonald
65k • written 4 days ago by
bandconductor
• 0
1
vote
2
replies
175
views
Design Matrix within group comparison more than two groups
DESeq2
15 days ago • updated 14 days ago
hemantcnaik
• 0
1
vote
4
replies
174
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 5 days ago by
James W. MacDonald
65k • written 9 days ago by
Mirella Aurora
• 0
2
votes
2
replies
171
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 22 days ago by
ATpoint
★ 4.0k • written 23 days ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
170
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
5 days ago • updated 3 days ago
shuwangxinze1996
• 0
0
votes
2
replies
170
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
8 days ago • updated 6 days ago
catv
• 0
0
votes
2
replies
169
views
Minfi - estimatecellscount
min
minfi
29 days ago
clacarion
• 0
0
votes
2
replies
168
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
27 days ago • updated 26 days ago
Seongsu
• 0
0
votes
1
reply
167
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 19 days ago by
James W. MacDonald
65k • written 20 days ago by
BCS12
• 0
0
votes
2
replies
166
views
Gene Ontology doubt
microbiomeExplorer
27 days ago • updated 23 days ago
Bhawna
• 0
1
vote
1
reply
166
views
Differentially expressed genes in monocle pseudotime
monocle
updated 12 days ago by
Gordon Smyth
50k • written 14 days ago by
kthapa
• 0
0
votes
1
reply
161
views
DESeq2 gives an error and R crashes
DESeq2
17 days ago • updated 16 days ago
Shefali
• 0
1
vote
4
replies
160
views
minfi::read.metharray.exp
minfiData
minfi
updated 4 days ago by
Basti
▴ 780 • written 5 days ago by
clacarion
• 0
0
votes
1
reply
159
views
Convert transcriptomic bam to genomic bam?
ensembldb
transcriptome
genome
coordinateconversion
updated 26 days ago by
Michael Love
41k • written 29 days ago by
saadmurtazakhan
▴ 10
0
votes
4
replies
158
views
flowStats Search Error
flowStats
updated 11 days ago by
shepherl
3.8k • written 12 days ago by
tholmes
• 0
1
vote
1
reply
156
views
DESeq2 - Missing values in count matrix
DESeq2
updated 23 days ago by
James W. MacDonald
65k • written 23 days ago by
Hong Thu
• 0
2
votes
2
replies
155
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
15 days ago • updated 13 days ago
daniel.carbajo
• 0
0
votes
2
replies
154
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
25 days ago
michelafrancesconi8
• 0
2
votes
2
replies
152
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 8 days ago by
James W. MacDonald
65k • written 9 days ago by
sansan
• 0
2
votes
2
replies
152
views
[DiffBind] Obtaining normalization factors
DiffBind
15 days ago • updated 12 days ago
Henry
▴ 10
0
votes
1
reply
150
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 22 days ago by
Gordon Smyth
50k • written 22 days ago by
avery
• 0
0
votes
2
replies
150
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
24 days ago
Marianna
▴ 20
0
votes
2
replies
148
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 22 days ago by
James W. MacDonald
65k • written 22 days ago by
joshua.mannheimer
• 0
0
votes
4
replies
148
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
9 days ago
sropri
• 0
1
vote
3
replies
148
views
Different Shrunk Log2FC according with reference
DESeq2
updated 3 days ago by
Michael Love
41k • written 4 days ago by
andrebolerbarros
▴ 20
0
votes
1
reply
145
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 25 days ago by
James W. MacDonald
65k • written 27 days ago by
ja569116
• 0
0
votes
1
reply
145
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 18 days ago by
Michael Love
41k • written 18 days ago by
Adelaide
• 0
0
votes
3
replies
145
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 9 days ago by
Gordon Smyth
50k • written 9 days ago by
prity6459
• 0
0
votes
1
reply
139
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 13 days ago by
Guido Hooiveld
★ 3.9k • written 17 days ago by
Lucie
• 0
1
vote
1
reply
139
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
25 days ago
Layal
• 0
0
votes
1
reply
136
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 18 days ago by
James W. MacDonald
65k • written 18 days ago by
zh9118
• 0
0
votes
0
replies
134
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
22 days ago
andromeda
• 0
3
votes
1
reply
134
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 9 days ago by
Gordon Smyth
50k • written 10 days ago by
Shaimaa Gamal
• 0
1
vote
3
replies
133
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 1 day ago by
Michael Love
41k • written 2 days ago by
JalapenoCornbread
• 0
1
vote
2
replies
130
views
Error in champ.load(): The following specified files do not exist
ChAMP
10 days ago • updated 9 days ago
Sherin
• 0
0
votes
1
reply
129
views
Adding columns to DEXSeqResults object
DEXSeq
updated 9 days ago by
Alejandro Reyes
★ 1.9k • written 11 days ago by
Clyde
• 0
0
votes
1
reply
129
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 25 days ago by
James W. MacDonald
65k • written 26 days ago by
Reeya
• 0
0
votes
1
reply
127
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 12 days ago by
kamryncole1963
• 0 • written 16 days ago by
Sara
• 0
0
votes
0
replies
127
views
Job:
PhD-position in bioinformatics / computational biology
Mergeomics
Epigenome
Evolution
NGS
Aging
19 days ago
arne.sahm
• 0
0
votes
1
reply
126
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 17 days ago by
ATpoint
★ 4.0k • written 19 days ago by
Merav
• 0
0
votes
1
reply
124
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 9 days ago by
ATpoint
★ 4.0k • written 10 days ago by
quanah.hudson
• 0
0
votes
2
replies
124
views
PCA plot suggestions
DESeq2
PCAtools
updated 1 day ago by
Michael Love
41k • written 3 days ago by
Aaliya
• 0
0
votes
1
reply
121
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 11 days ago by
James W. MacDonald
65k • written 14 days ago by
tian.liu0720
• 0
0
votes
1
reply
121
views
Bioinformatics student
Des
DESeq2
updated 15 days ago by
hemantcnaik
• 0 • written 15 days ago by
Sahar
• 0
0
votes
1
reply
119
views
Granges regionCounts not returning the expected number of entries
methylKit
23 days ago • updated 22 days ago
Modoc Kesner
▴ 10
0
votes
1
reply
117
views
covariate with negative and positive values
DESeq2
updated 9 days ago by
Michael Love
41k • written 11 days ago by
Brynn
• 0
193 results • Page
3 of 4
Recent ...
Replies
Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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