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Creation
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Votes
1
vote
4
replies
3.2k
views
How to find the end position of a read?
rsamtools
alignment
cigar
8.6 years ago
Frocha
▴ 20
1
vote
1
reply
1.6k
views
How to normalization counts matrix by GC content and sizeFactors using DESeq2 and CQN?
deseq2
cqn
updated 8.6 years ago by
Michael Love
43k • written 8.6 years ago by
984366176
▴ 10
0
votes
0
replies
1.4k
views
xcmsFragments extract product fragment
xcms
xcms2
8.6 years ago
riccardo.romoli
• 0
0
votes
3
replies
1.6k
views
CRISPRseek with Doench 2016 scores
crisprseek
updated 8.6 years ago by
Julie Zhu
★ 4.3k • written 8.6 years ago by
pavitrarc
▴ 20
0
votes
1
reply
1.3k
views
RNAseq Analysis using RUVs
rnaseq
ruvseq
r
updated 8.6 years ago by
davide risso
▴ 980 • written 8.6 years ago by
manish20072013
• 0
0
votes
2
replies
1.4k
views
Filter CNVs if contain certain gene
cnv
genomic ranges
cnvs
8.6 years ago
julrodr80
▴ 30
0
votes
6
replies
2.5k
views
Different results obtained from mroast and camera from Deseq2 counts
limma
camera
mroast
tximport
updated 8.6 years ago by
James W. MacDonald
68k • written 8.6 years ago by
jarod_v6@libero.it
▴ 40
4
votes
7
replies
7.0k
views
BiocParallel/scater warning after move to R 3.4.0
biocparallel
scater
updated 8.6 years ago by
andrew.blake
▴ 40 • written 8.8 years ago by
nhejazi
• 0
0
votes
0
replies
1.4k
views
bsseq - dmrFinder error
bsseq r package
bsmooth
dmrFinder
8.6 years ago
parker
• 0
1
vote
2
replies
1.7k
views
qvalues lower than pvalues
qvalue
8.6 years ago
AR3513
• 0
0
votes
1
reply
1.6k
views
EdgeR dispersion and FDR
edger
FDR
rnaseq
updated 8.6 years ago by
Aaron Lun
★ 29k • written 8.6 years ago by
dsarbashis
• 0
2
votes
9
replies
24k
views
DESeq2 Error: ncol(countData) == nrow(colData) is not TRUE
deseq2
error
updated 4.4 years ago by
Michael Love
43k • written 8.6 years ago by
anpham
▴ 70
0
votes
1
reply
818
views
How to install BiocInstaller_1.22.3 on mac OSX yosemite
R
updated 8.6 years ago by
Mike Smith
★ 6.6k • written 8.6 years ago by
nakanomasayuki265
• 0
3
votes
1
reply
1.7k
views
ReactomePA enrichMap function - a question regarding the connections between nodes
reactomepa
updated 8.6 years ago by
Lluís Revilla Sancho
▴ 760 • written 8.6 years ago by
juls
• 0
0
votes
1
reply
1.5k
views
plotMutationSpectrum Colour By Patient with Multiple Samples
plotMutationSpectrum
somaticsignatures
somaticsignatures package
updated 8.6 years ago by
Julian Gehring
★ 1.3k • written 8.6 years ago by
bruce.moran
▴ 30
0
votes
0
replies
1.6k
views
How to generate CpG island Unmasked.bed file format for finding CpG island shores and shelves?
bioconductor
annotation
rtracklayer
genomes
homo.sapiens
8.6 years ago
sivabala76
• 0
0
votes
4
replies
1.8k
views
how to install AnnotationHub_2.4.2
R
updated 8.6 years ago by
Martin Morgan
25k • written 8.6 years ago by
nakanomasayuki265
• 0
2
votes
3
replies
1.3k
views
R package tarball size
R
bioconductor
8.6 years ago
Mohamad S. Hasan
• 0
0
votes
0
replies
1.1k
views
Get bugs from pathview package
pathview
8.6 years ago
joseph
▴ 50
0
votes
2
replies
1.7k
views
sortSeqlevels is not sorting for GRanges object
GRanges
updated 8.6 years ago by
Michael Lawrence
★ 11k • written 8.6 years ago by
Haiying.Kong
▴ 110
5
votes
9
replies
2.7k
views
reduce function after combining 2 GRanges objects from cn.mops output
GRanges
cn.mops
updated 8.6 years ago by
Michael Lawrence
★ 11k • written 8.6 years ago by
Haiying.Kong
▴ 110
0
votes
1
reply
2.1k
views
How to generate heatmap for three groups
rnaseq
ruvseq
heatmap
updated 8.6 years ago by
James W. MacDonald
68k • written 8.6 years ago by
manish20072013
• 0
0
votes
2
replies
4.0k
views
Time-course analysis with limma for >3 time points
limma
contrast matrix
design matrix
multiple time points
timecourse
updated 4.8 years ago by
rf
• 0 • written 8.6 years ago by
relathman
▴ 20
0
votes
2
replies
1.8k
views
How to know which Microarray Technique was used to processes the files
R
microarray
affymetrix microarrays
updated 8.6 years ago by
Axel Klenk
★ 1.1k • written 8.6 years ago by
g.k
• 0
3
votes
2
replies
3.3k
views
How do I clean .git folder?
Git
github
updated 8.6 years ago by
Martin Morgan
25k • written 8.6 years ago by
Mohamad S. Hasan
• 0
4
votes
4
replies
1.6k
views
Does anyone need to install an R package which is used by another package as importFrom(.,.)?
R
updated 8.6 years ago by
Lluís Revilla Sancho
▴ 760 • written 8.6 years ago by
Mohamad S. Hasan
• 0
2
votes
5
replies
4.2k
views
Error in GenomeInfoDb:::getDanglingSeqlevels
ggbio
8.6 years ago
Bogdan
▴ 670
0
votes
2
replies
1.5k
views
ChIPQC plots for input samples
chipqc
updated 8.6 years ago by
Thomas Carroll
▴ 420 • written 8.6 years ago by
C T
▴ 140
0
votes
3
replies
1.7k
views
ChIPQC reading more samples that it should
chipqc
8.6 years ago
C T
▴ 140
0
votes
2
replies
1.1k
views
How to set the amount of RAM used for Package 'BCRANK' ?
chipseq
BCRANK
updated 8.6 years ago by
James W. MacDonald
68k • written 8.6 years ago by
rezapanahi222
• 0
1
vote
3
replies
1.7k
views
ChIPQC : ChIPQCreport(dba_object) getting error when drawing plotFribl
ChIPQC
8.6 years ago
ZheFrench
▴ 60
0
votes
3
replies
2.2k
views
unable to install GenomeWideSNP_6 cdf
makecdfenv
bioclite
updated 8.6 years ago by
James W. MacDonald
68k • written 8.6 years ago by
vinaysbharadhwaj
• 0
0
votes
1
reply
1.2k
views
summarizeVariants from VariantAnnotation reordering genes in rownames
variantannotation
summarizevariants
updated 8.6 years ago by
Valerie Obenchain
★ 6.8k • written 8.7 years ago by
Todd Creasy
• 0
2
votes
1
reply
1.5k
views
How to combine CNVDetectionResult objects in cn.mops package
cn.mops
updated 8.6 years ago by
Günter Klambauer
▴ 540 • written 8.6 years ago by
Haiying.Kong
▴ 110
3
votes
4
replies
4.6k
views
How to convert a DnaStringSet object to list of seq?
dnastringset
list
stringset
updated 8.6 years ago by
Martin Morgan
25k • written 8.6 years ago by
vinod.acear
▴ 50
0
votes
3
replies
1.9k
views
kegga() p-value calculated differently in different edgeR versions
edger
kegga
updated 8.6 years ago by
Gordon Smyth
53k • written 8.6 years ago by
cronanz
• 0
0
votes
0
replies
1.5k
views
segfault when trying to convert hta20_Hs_ENSE_22.cdf to binary format
affxparser
cdf
hta2.0
8.6 years ago
relathman
▴ 20
1
vote
5
replies
2.7k
views
Error creating DESeqDataSet from "airway" SummarizedExperiment
deseq2
genomicranges
updated 8.6 years ago by
Hervé Pagès
16k • written 8.6 years ago by
Levi Waldron
★ 1.1k
0
votes
2
replies
1.6k
views
Human reference primary assembly and masking using BioStrings and BSgenome
biostrings
R
bsgenome
8.6 years ago
rockyb
• 0
0
votes
5
replies
5.6k
views
odd results "No enrichment found in any of gene cluster"
clusterprofiler
updated 8.6 years ago by
Guangchuang Yu
★ 1.2k • written 8.6 years ago by
joseph
▴ 50
4
votes
2
replies
4.4k
views
Difference between "be" and "leek" methods when deciding number of surrogate variables to estimate with SVA?
sva
num.sv
8.6 years ago
brhead
▴ 40
1
vote
2
replies
2.5k
views
AnnotationForge makeOrgPackage rsqlite_send_query error
annotationforge
makeorgpackage
updated 16 days ago by
ansley.r.burtch
• 0 • written 8.6 years ago by
marisa.e.miller
▴ 10
0
votes
1
reply
3.0k
views
R Session Aborted; R ecountered a fatal error while loading openCyto
opencyto
fatal error
library
updated 8.6 years ago by
Jiang, Mike
★ 1.3k • written 8.6 years ago by
Maria
• 0
2
votes
2
replies
2.9k
views
EdgeR -ANOVA-like test vs testing individual contrasts
EdgeR
ANOVA
t-test
contrast
updated 8.6 years ago by
Aaron Lun
★ 29k • written 8.6 years ago by
Maiv
• 0
0
votes
2
replies
1.8k
views
How do you show/export color scale of a heatmap generated by plotMRheatmap of metagenomeSeq?
metagenomeseq
plotmrheatmap
color key
8.6 years ago
chawonhe
• 0
0
votes
1
reply
1.9k
views
How to generate CpG island Unmasked.bed file format for finding CpG island shores and shelves?
annotation
8.6 years ago
sivabala76
• 0
0
votes
0
replies
1.3k
views
Differential expressed genes between different samples in RUVseq
rnaseq
ruv
differential gene expression
R
8.6 years ago
manish20072013
• 0
0
votes
1
reply
3.0k
views
Unable to perform analysis on all the chromosomes with the latest version of ChIPQC 1.12
chipqc
R
updated 8.6 years ago by
Thomas Carroll
▴ 420 • written 8.7 years ago by
tuteja.reetu
• 0
0
votes
1
reply
1.5k
views
Correlate drugs to diseases using DrugVsDisease data
drugvsdisease
drug
disease
updated 8.6 years ago by
saezrodriguez
• 0 • written 8.7 years ago by
bioinformatics
▴ 30
6
votes
4
replies
3.7k
views
Identification of DEGs through limma analysis
limma
microarray
DEGs
p values
lfc
8.7 years ago • updated 8.6 years ago
rkp
• 0
46,750 results • Page
325 of 935
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Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2
by
colinmccornack
• 0
FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name
by
Erik Wright
▴ 150
This has to do with the fact that some taxonomies reuse names at the same rank level. Common examples in the SILVA taxonomy are "Incertae S…
Comment: Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
by
a2a2ddrhaa
• 0
For those taking a break from the lab, the CT777 Game download https://ct7777.pk/ offers a high-performance entry into online mobile gaming…
Answer: Subsetting data verses contrasts [DESeq2]?
by
ATpoint
★ 5.0k
This has been asked many times before, please search for relevant posts. In short: Generally it is least tedious to not split the data and …
Comment: Bulk RNAseq analysis for
by
Mariami
• 0
Thank you so much for your help! will try to proceed with the suggestion
Votes
Answer: Can you colour dendrogram branch clusters in pheatmap?
Comment: Are transformed values from rlog /vst log2 normalized counts?
Are transformed values from rlog /vst log2 normalized counts?
Answer: Bulk RNAseq analysis for
Answer: DiffBind differential analysis
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