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News:
Legacy Bioconductor Installation
Installation
Bioconductor
2 hours ago
shepherl
3.9k
0
votes
1
reply
22
views
GSVA function
DESeq2
GSVA
ssGSEA
updated 2 hours ago by
Robert Castelo
★ 3.3k • written 4 hours ago by
michelafrancesconi8
• 0
0
votes
3
replies
39
views
Cannot install oligo on Fedora
oligo
source
Install
updated 1 hour ago by
James W. MacDonald
66k • written 4 hours ago by
Guido Hooiveld
★ 4.0k
0
votes
1
reply
37
views
Normalisation using clinical traits in RNA seq using DESeq2
DESeq2
clinicaltraits
Normalization
batchnormalisation
updated 8 hours ago by
ATpoint
★ 4.2k • written 9 hours ago by
sukeshinik5
• 0
0
votes
0
replies
12
views
News:
Online course: Network Analysis in Systems Biology with R/Bioconductor
SystemsBiology
Bioconductor
Network
9 hours ago
info
▴ 10
0
votes
2
replies
48
views
Cluster columns in Pheatmap
geneexp
pheatmap
heatmaps
cluster
updated 6 hours ago by
James W. MacDonald
66k • written 9 hours ago by
pehove2385
• 0
0
votes
2
replies
75
views
Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 20 hours ago by
Michael Love
42k • written 21 hours ago by
tjl
• 0
0
votes
1
reply
39
views
Error when running topGO with KS statistic and elim agorithm
topGO
updated 5 hours ago by
James W. MacDonald
66k • written 22 hours ago by
adendekk
• 0
0
votes
0
replies
22
views
News:
Bioconductor Build System
Builds
Bioconductor
1 day ago
shepherl
3.9k
0
votes
0
replies
27
views
News:
BioC2024 Bioconductor Carpentries RNA-Seq Workshop July 22-23
BioC2024
Conference
Bioconductor
Community
1 day ago
Maria Doyle
▴ 70
0
votes
4
replies
222
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq
Rsubread
updated 12 hours ago by
Wei Shi
★ 3.6k • written 1 day ago by
atan
• 0
0
votes
0
replies
18
views
Job:
Bioinformatics MSc University of York
bioinformatics
JobPosting
1 day ago
Daphne
• 0
2
votes
2
replies
88
views
unable to access bioconductor packages - qvalue installation failed...
Install
updated 1 day ago by
shepherl
3.9k • written 1 day ago by
gabry.scata
▴ 10
5
votes
6
replies
281
views
Not able to install any Bioconductor 3.18 package [unable to access index]
Install
updated 1 day ago by
merv
▴ 120 • written 1 day ago by
Lorena Pantano
▴ 140
2
votes
2
replies
71
views
Get gene symbols for a set of hg19 coordinates
annotation
hg19
1 day ago
pcantalupo
▴ 10
2
votes
4
replies
142
views
Help with infinite recursion - non-zero exit status in installation of GenomeInfoDbData
Install
GenomeInfoDbData
GenomeInfoDb
updated 1 day ago by
James W. MacDonald
66k • written 2 days ago by
Brandon
▴ 20
1
vote
8
replies
146
views
Slightly different count plots from R and spreadsheet
DESeq2
ggplot2
2 days ago • updated 1 day ago
boczniak767
▴ 720
0
votes
0
replies
30
views
Problem in execuation of filterAndTrim command in DADA2
Bioconductor
dada2
2 days ago • updated 1 day ago
abhisek001
• 0
0
votes
3
replies
106
views
pathview error
KEGGgraph
KEGG
updated 1 day ago by
Guido Hooiveld
★ 4.0k • written 2 days ago by
Fara
• 0
0
votes
5
replies
255
views
Running ENmix with mouse methylation manifest: readidat error - Error in readmanifest(manifestfile) : length(control.line) == 1 && is.integer(cont…
ENmix
Bioconductor
updated 1 day ago by
xuz
• 0 • written 3 days ago by
minardsmitha
▴ 10
4
votes
3
replies
148
views
recount3 problem downloading data from source sra
recount3
updated 1 day ago by
Leonardo Collado Torres
★ 1.1k • written 3 days ago by
PABLO ANTONIO
▴ 10
0
votes
0
replies
36
views
Conditional analysis
GENESIS
3 days ago
SuperDad
• 0
0
votes
0
replies
37
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq
peaks
ATAC
ChIPpeakAnno
3 days ago
Raghad
• 0
2
votes
2
replies
118
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools
limma
ExpressionData
RNASeq
edgeR
3 days ago • updated 2 days ago
mohammedtoufiq91
▴ 10
1
vote
1
reply
81
views
Documenting resources in an `ExperimentHub` package?
AnnotationHub
ExperimentHub
updated 3 days ago by
James W. MacDonald
66k • written 3 days ago by
Tim Barry
• 0
0
votes
2
replies
107
views
Errors in chromosome annotation-biomaRt
org.Rn.eg.db
biomaRt
4 days ago • updated 1 day ago
landenshanie
▴ 40
0
votes
0
replies
31
views
Job:
Post-Doc: Development of a new method to study the distribution of the effect sizes of QTL
StatisticalMethod
Evolution
QuantitativeTrailLocus
Genetics
JobPosting
4 days ago
pierre.devillemereuil
• 0
1
vote
1
reply
88
views
Control group between 2 batches have different expression in RNAseq data
BatchQC
BatchEffect
rnaseqGene
Normalization
updated 4 days ago by
James W. MacDonald
66k • written 4 days ago by
Đình Vinh
• 0
0
votes
0
replies
12
views
Spam:
Understanding Laser Hair Removal?
healthyControlsPresenceChecker
4 days ago
shahrozimmac
0
1
vote
1
reply
188
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC
BatchEffect
RNASeq
updated 4 days ago by
James W. MacDonald
66k • written 4 days ago by
ttt
• 0
0
votes
0
replies
40
views
Processing of curatedmetagenomics
curatedMetagenomicData
4 days ago
Edward
• 0
1
vote
3
replies
145
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 4 days ago by
James W. MacDonald
66k • written 5 days ago by
boczniak767
▴ 720
1
vote
2
replies
92
views
How to run allelic imbalance in apeglm
apeglm
updated 4 days ago by
Michael Love
42k • written 5 days ago by
euge.eugenio
▴ 20
0
votes
0
replies
46
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq
scRNAseq
5 days ago
Bibi
• 0
0
votes
5
replies
188
views
all variables in design formula must be columns in colData (Deseq2) error
BatchQC
batchinDeseq2.
columnsincolData.
5 days ago • updated 4 days ago
Galina
• 0
1
vote
2
replies
125
views
Subsetting RNAseq data | voomaByGroup()
limma
6 days ago • updated 4 days ago
Anna
• 0
0
votes
1
reply
84
views
ERROR; return code from pthread_create() is 22
affy
updated 4 days ago by
James W. MacDonald
66k • written 6 days ago by
pickingastar
• 0
0
votes
0
replies
56
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets
allele_freq
biomaRt
getBM
6 days ago • updated 5 days ago
Abiologist
• 0
2
votes
4
replies
219
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
updated 4 days ago by
Michael Love
42k • written 7 days ago by
shaunpeterson
• 0
0
votes
3
replies
143
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 7 days ago by
damian.szk
▴ 80 • written 7 days ago by
ninidea
• 0
0
votes
6
replies
605
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
7 days ago • updated 4 days ago
Ken C
• 0
0
votes
2
replies
145
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
8 days ago
makala
• 0
0
votes
0
replies
73
views
determine k during RUVSeq
RUVSeq
RUVnormalize
8 days ago
Ειρήνη
• 0
0
votes
0
replies
74
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
8 days ago
Shaimaa Gamal
• 0
0
votes
0
replies
16
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
8 days ago
oliverelijhan
0
0
votes
0
replies
96
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
8 days ago
Anton01
• 0
2
votes
3
replies
188
views
Problem installing ChAMP on a MacBook
ChAMP
updated 8 days ago by
shepherl
3.9k • written 8 days ago by
Galia
• 0
0
votes
0
replies
69
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
8 days ago
danalvoronov
▴ 10
0
votes
0
replies
65
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
8 days ago
k200987
• 0
2
votes
5
replies
268
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db
Bioconductor
9 days ago • updated 7 days ago
Patadù
▴ 10
1,000 results • Page
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Replies
Comment: Cannot install oligo on Fedora
by
James W. MacDonald
66k
There is the `zlibbioc` package that provides the headers for zlib 1.2.5, that I think you should be able to use, although that would requi…
Answer: GSVA function
by
Robert Castelo
★ 3.3k
Hi, We recommend to input normalized expression values in logarithmic scale to GSVA. We also recommend to use the latest release of the …
Comment: Cannot install oligo on Fedora
by
Guido Hooiveld
★ 4.0k
Aha, that is a good one! Starting from release 40, as I just found out, Fedora apparently is not including/using `zlib` as such anymore, b…
Comment: Cannot install oligo on Fedora
by
James W. MacDonald
66k
What version of zlib are you running? I can compile with 1.2.7
Comment: SingleR Label.Ont
by
Anna
• 0
It makes me happy that I have finally found a trusted and safe online casino in Australia. I read a lot of different additional information…
Votes
Answer: How to run allelic imbalance in apeglm
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Answer: Documenting resources in an `ExperimentHub` package?
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Seurat/DESeq2 - single cell RNA-seq differential expression
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