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127
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray
cdf
crlmm
6 weeks ago
mayra.haedo
• 0
0
votes
0
replies
112
views
Macsquant FCS in read.FCS & opencyto
FlowCytometry
flowWorkspace
flowCore
6 weeks ago
taylor.witte
• 0
0
votes
0
replies
138
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
6 weeks ago
erbrocato
• 0
1
vote
4
replies
286
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
6 weeks ago
samuel.channon
• 0
0
votes
2
replies
199
views
Visium RNA
metaMSdata
updated 6 weeks ago by
vvvc360work2
• 0 • written 6 weeks ago by
Karlison
• 0
1
vote
2
replies
283
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 6 weeks ago by
ATpoint
★ 4.1k • written 6 weeks ago by
maximilian.beikirch
• 0
0
votes
0
replies
115
views
DNAcopy segment function not reproducible even when setting seed
DNAcopy
6 weeks ago
BID
• 0
1
vote
3
replies
270
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 5 weeks ago by
mercedeh.movassagh
▴ 10 • written 6 weeks ago by
María
• 0
0
votes
2
replies
243
views
Error in msaFun Cannot open input file. No alignment!
msa
written 6 weeks ago by
Kamil Slowikowski
▴ 30
0
votes
1
reply
195
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
updated 5 weeks ago by
Guido Hooiveld
★ 3.9k • written 6 weeks ago by
Julie
• 0
0
votes
1
reply
178
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Gerhard Thallinger
▴ 180
0
votes
2
replies
240
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
7 weeks ago
Sam
▴ 10
0
votes
1
reply
226
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks
TCGA
clinical
TCGA-BRCA
written 7 weeks ago by
BioinfoMug
• 0
0
votes
1
reply
194
views
Exact same results in Diffbind with different normalization methods
DiffBind
7 weeks ago • updated 6 weeks ago
red_bricks
▴ 50
0
votes
0
replies
132
views
FELLA plotGraph function won't change the legend
FELLA
7 weeks ago
yuhang
• 0
0
votes
0
replies
145
views
medips-output
ngsReports
MEDIPS
7 weeks ago
subhiksha
• 0
0
votes
0
replies
135
views
Join BOC Sciences at Drug Discovery Chemistry
alabaster.schemas
db0
7 weeks ago
bocsci11
• 0
0
votes
0
replies
111
views
The graphical interface of FELLA doesn't work
FELLA
7 weeks ago
yuhang
• 0
0
votes
0
replies
131
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
7 weeks ago
jean-christophe.helbling
• 0
0
votes
0
replies
150
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
7 weeks ago
Henry
• 0
0
votes
1
reply
214
views
Rcpp compilation error
Release
Rcpp
updated 7 weeks ago by
ATpoint
★ 4.1k • written 7 weeks ago by
Robert K. Bradley
▴ 40
0
votes
0
replies
173
views
Rain error: invalid annotation of time points
rain
7 weeks ago
mpuli011
• 0
0
votes
0
replies
185
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi
minfiDataEPIC
7 weeks ago
Felix
• 0
0
votes
0
replies
145
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
8 weeks ago • updated 6 weeks ago
Giovanni Calice
▴ 160
0
votes
0
replies
195
views
Error: grouping factors must have > 1 sampled level
Mast
mastR
MAST
updated 8 weeks ago by
James W. MacDonald
65k • written 8 weeks ago by
Andrew
• 0
0
votes
0
replies
142
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
8 weeks ago
chris2.a.white
• 0
0
votes
0
replies
159
views
Could SGSeq utilizes "ts" tag produced from minimap2 other than "XS" tag?
XS-tag
SplicedAlignment
SGSeq
minimap2
8 weeks ago
jk
• 0
0
votes
0
replies
148
views
Can I combine collinear variables into a single value
BatchEffect
limma
8 weeks ago
Harrsha
• 0
0
votes
0
replies
227
views
Error in set(x, j = name, value = value) : Supplied 52 items to be assigned to 55 items of column 'locus'. If you wish to 'recycle' the RHS please…
ASpli
8 weeks ago
vipul14
• 0
0
votes
0
replies
115
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R
ATACseqQC
8 weeks ago
danalvoronov
▴ 10
0
votes
0
replies
139
views
lfcSE
RGSEA
9 weeks ago
Gordon
• 0
0
votes
4
replies
293
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
9 weeks ago • updated 8 weeks ago
mperalc
• 0
1
vote
0
replies
169
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k
MethylationArray
TCGAbiolinks
Tcga
TCGAbiolinksGUI.data
9 weeks ago
BioinfoMug
• 0
0
votes
0
replies
158
views
Unclear exon-exon connection after RSubjunc() usage
IGV
Rsubjunc
Rsubread
9 weeks ago
thomas.heigl.ibk
• 0
0
votes
1
reply
246
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 9 weeks ago by
ATpoint
★ 4.1k • written 9 weeks ago by
sodiogoes
• 0
0
votes
6
replies
700
views
StringDB: Cannot finish their tutorial because of an error
STRINGdb
updated 7 weeks ago by
qianyi13
• 0 • written 9 weeks ago by
Pavel
• 0
0
votes
2
replies
313
views
problem in installing the new version of bioconductor
ANCOMBC
updated 9 weeks ago by
shepherl
3.8k • written 9 weeks ago by
Maryam
• 0
0
votes
0
replies
168
views
Comparing the effects of a condition over time in two seperate tissues
MAST
10 weeks ago
Dillon
• 0
0
votes
4
replies
341
views
Installation problem of rtracklayer on Bioconductor version 3.19
newpackage
rtracklayer
updated 10 weeks ago by
shepherl
3.8k • written 10 weeks ago by
Lucille
• 0
0
votes
3
replies
244
views
problems updating package
TrajectoryGeometry
10 weeks ago
michael.shapiro
• 0
0
votes
0
replies
206
views
how to solve this error?
ChAMPdata
ChAMP
10 weeks ago
Meghana
• 0
1
vote
1
reply
257
views
FCS3.2 reading
flowWorkspace
flowCore
CytoML
updated 5 weeks ago by
SamGG
▴ 350 • written 10 weeks ago by
jarod
▴ 30
0
votes
0
replies
164
views
flowAI: flow rare check in R vs FlowJo
flowAI
10 weeks ago
Olena
• 0
0
votes
0
replies
198
views
ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
10 weeks ago
mat149
▴ 70
0
votes
0
replies
165
views
GDC slides download
TCGAbiolinks
10 weeks ago
jain72744
• 0
0
votes
0
replies
218
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
11 weeks ago
Abril
• 0
0
votes
4
replies
292
views
I need to calculate the survival rate of TCGA databases
TCGAbiolinks
Survival
updated 11 weeks ago by
Lluís Revilla Sancho
▴ 730 • written 11 weeks ago by
tirordep
• 0
0
votes
1
reply
218
views
"Counts" in enrichGO
GSEABase
updated 11 weeks ago by
Tyler Sagendorf
▴ 10 • written 11 weeks ago by
Matthew
• 0
0
votes
1
reply
262
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor
WGCNA
updated 11 weeks ago by
ATpoint
★ 4.1k • written 11 weeks ago by
Priya
• 0
2
votes
15
replies
687
views
Problems with enrichGO
clusterProfiler
enrichGO
updated 11 weeks ago by
Michael Love
41k • written 11 weeks ago by
cinzia.spagnoli
• 0
1,000 results • Page
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Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq
by
james.zhang20
• 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Comment: Deseq2 and Normalization of RNA sequencing data
by
ATpoint
★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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