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votes
0
replies
7
views
PCA plot suggestions
DESeq2
PCAtools
1 hour ago
Aaliya
• 0
0
votes
7
replies
149
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
1 day ago • updated 1 hour ago
Aaliya
• 0
0
votes
2
replies
78
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
2 days ago • updated 2 hours ago
shuwangxinze1996
• 0
1
vote
13
replies
240
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
3 days ago • updated 8 hours ago
fernanda.backsouza
▴ 10
0
votes
0
replies
14
views
ATACseq merge peaks
DiffBind
12 hours ago • updated 11 hours ago
Shloka
• 0
0
votes
0
replies
12
views
Differential splicing from SGSeq analysis
DEXSeq
SGSeq
14 hours ago • updated 13 hours ago
Sara
• 0
0
votes
0
replies
22
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
16 hours ago
Dario Strbenac
★ 1.5k
1
vote
0
replies
32
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
18 hours ago
ATpoint
★ 4.0k
1
vote
3
replies
810
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 19 hours ago by
Guangchuang Yu
★ 1.2k • written 13 months ago by
ruiqi.li
▴ 10
0
votes
0
replies
40
views
Improving the design matrices vignette in RNAseq123
RNAseq123
2 days ago
Lluís Revilla Sancho
▴ 730
0
votes
0
replies
39
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
3 days ago
vaxahey107
• 0
0
votes
0
replies
61
views
I am trying to detect alternative splicing.
ASpli
4 days ago
Sebashish
• 0
0
votes
4
replies
193
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
7 days ago • updated 4 days ago
lonn
• 0
0
votes
2
replies
234
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
24 days ago • updated 5 days ago
isaac.vock
• 0
1
vote
2
replies
179
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
6 days ago
Le
• 0
0
votes
3
replies
221
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 6 days ago by
W. Evan Johnson
▴ 850 • written 12 days ago by
schlumbohm
• 0
0
votes
0
replies
85
views
Warning while loading DEP package
DEP
updated 6 days ago by
shepherl
3.8k • written 6 days ago by
Namrata
• 0
1
vote
2
replies
124
views
Error in champ.load(): The following specified files do not exist
ChAMP
7 days ago • updated 6 days ago
Sherin
• 0
0
votes
1
reply
78
views
Input Question for deseq.r
RSeqAn
updated 6 days ago by
ATpoint
★ 4.0k • written 7 days ago by
Nina
• 0
1
vote
7
replies
1.7k
views
Error using champ.import
ChAMP
EPICv2
updated 7 days ago by
shilpa
• 0 • written 9 months ago by
medha.suman
• 0
0
votes
0
replies
51
views
Enzyme Engineering
BioTIP
7 days ago
bocchemistry
• 0
0
votes
0
replies
76
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
8 days ago
Maliha Tabassum
• 0
0
votes
1
reply
98
views
what is the sampleFiles
chipseq
updated 8 days ago by
James W. MacDonald
65k • written 8 days ago by
zhulin
• 0
2
votes
2
replies
144
views
[DiffBind] Obtaining normalization factors
DiffBind
12 days ago • updated 8 days ago
Henry
▴ 10
0
votes
0
replies
76
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
9 days ago
Virangika
• 0
0
votes
0
replies
57
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
9 days ago
Henry
▴ 10
0
votes
1
reply
109
views
Deseq2 Rlog transformation
DESeq2
updated 9 days ago by
ATpoint
★ 4.0k • written 10 days ago by
Sahar
• 0
0
votes
1
reply
132
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 10 days ago by
Guido Hooiveld
★ 3.9k • written 14 days ago by
Lucie
• 0
0
votes
0
replies
73
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
12 days ago
Stevie Pederson
• 0
0
votes
1
reply
154
views
DESeq2 gives an error and R crashes
DESeq2
14 days ago • updated 13 days ago
Shefali
• 0
3
votes
6
replies
230
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
13 days ago
nhaus
▴ 30
0
votes
0
replies
111
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
14 days ago
Eryn
• 0
0
votes
0
replies
76
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
14 days ago
Dennis
• 0
0
votes
1
reply
323
views
Gene names from Matrix
BioCor
StarBioTrek
MatrixGenerics
updated 14 days ago by
Lluís Revilla Sancho
▴ 730 • written 6 months ago by
karmasstark
• 0
0
votes
0
replies
90
views
ggtree tip label position (depth)
ggtree
15 days ago • updated 14 days ago
Roope
• 0
0
votes
1
reply
493
views
Cibersort phenotype file
cibersort
deconvR
immune
updated 15 days ago by
ivorychan7777
• 0 • written 14 months ago by
609b0d25
• 0
2
votes
6
replies
342
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
16 days ago
Chris
• 0
0
votes
1
reply
115
views
Granges regionCounts not returning the expected number of entries
methylKit
20 days ago • updated 19 days ago
Modoc Kesner
▴ 10
0
votes
1
reply
537
views
CopywriteR output
CopywriteR
updated 19 days ago by
fer_talavera
• 0 • written 2.5 years ago by
Joshua
• 0
0
votes
2
replies
273
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
24 days ago • updated 19 days ago
fer_talavera
• 0
0
votes
0
replies
129
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
19 days ago
andromeda
• 0
0
votes
0
replies
84
views
flowDensity on a flowset
flowDensity
20 days ago
fredrikwallberg
• 0
0
votes
0
replies
78
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
21 days ago
Macsue
• 0
0
votes
1
reply
140
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 22 days ago by
James W. MacDonald
65k • written 24 days ago by
ja569116
• 0
0
votes
7
replies
346
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
25 days ago • updated 22 days ago
needNGS
• 0
0
votes
3
replies
312
views
Statistical test
NewWave
written 4 months ago by
mario
• 0
1
vote
5
replies
298
views
fgsea fork
fgsea
updated 26 days ago by
James W. MacDonald
65k • written 27 days ago by
yimjohns
• 0
0
votes
0
replies
96
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
26 days ago
feather-W
• 0
0
votes
0
replies
95
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
26 days ago
Ankit
▴ 20
0
votes
0
replies
83
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
27 days ago
Pierre Lindenbaum
▴ 10
1,000 results • Page
1 of 20
Recent ...
Replies
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
shuwangxinze1996
• 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough?
Comment: DESeq2 output used for PCA plot on R studio
by
Kevin Blighe
★ 3.9k
This comment helps.
Comment: DESeq2 output used for PCA plot on R studio
by
Kevin Blighe
★ 3.9k
I am not sure how your comment helps here?
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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