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0
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415
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Is there a Bioconductor package to calculate TFs regulatory networks?
TFs
Transcription
regulator
22 months ago
OliverBoynton
• 0
0
votes
2
replies
1.9k
views
Getting annotation into GOstat
Transcription
Transcription
updated 6.2 years ago by
j.baldauf
• 0 • written 11.5 years ago by
Naomi Altman
★ 6.0k
0
votes
1
reply
1.1k
views
Reference annotation file contains only transcript and CDS information, how to analyze the different expression of genes?
transcription
hisat2
6.4 years ago
zoukai3412085
• 0
0
votes
0
replies
1.1k
views
Job:
PhD computational position - Milan
epigenetics
transcription
computational biology
Job
6.8 years ago
mattia pelizzola
▴ 200
1
vote
4
replies
1.2k
views
DESeq2: Tests of log2 differences
deseq2
rna-seq
transcription
dgea
6.9 years ago
fabian
▴ 40
1
vote
0
replies
917
views
Bioconductor for predicting transcription factors from a gene list?
transcription
transcriptdb
6.9 years ago
hkarakurt
▴ 20
0
votes
1
reply
1.3k
views
TF ANALYSIS USING JASPAR
transcription
jaspar
updated 7.0 years ago by
James W. MacDonald
65k • written 7.0 years ago by
nia
▴ 30
0
votes
3
replies
2.3k
views
Gramene now available via biomaRt
SNP
Transcription
biomaRt
Vega
SNP
Transcription
biomaRt
Vega
updated 7.5 years ago by
maialiaeb
• 0 • written 17.2 years ago by
Steffen Durinck
▴ 580
1
vote
0
replies
1.5k
views
News:
BioCAsia, 4th November 2016, Brisbane, Australia
conference
transcription
epigenomics
visualization
infrastructure
News
7.8 years ago
Matthew Ritchie
▴ 1000
3
votes
0
replies
1.7k
views
News:
BioCAsia, 8 Sept 2015, Tokyo
sequencing
transcription
epigenomics
visualization
infrastructure
News
8.8 years ago • updated 8.7 years ago
Matthew Ritchie
▴ 1000
0
votes
2
replies
3.8k
views
Bioconductor 2.12 is released
BiocViews
aCGH
SNP
Transcription
Sequencing
Microarray
Coverage
Alignment
Annotation
GO
updated 8.8 years ago by
marksteve952
• 0 • written 11.0 years ago by
Dan Tenenbaum
★ 8.2k
4
votes
0
replies
1.5k
views
News:
Hands-on Bioconductor course, 7 Sept 2015, Tokyo
sequencing
transcription
variantfiltering
annotation
News
8.8 years ago
Matthew Ritchie
▴ 1000
0
votes
1
reply
2.5k
views
Interspecies differential expression of orthologs with Edger
Transcription
edgeR
Transcription
edgeR
9.7 years ago • updated 9.6 years ago
Tim Triche
★ 4.2k
0
votes
11
replies
2.1k
views
Interspecies differential expression of orthologs with Edger
Transcription
edgeR
Transcription
edgeR
updated 9.7 years ago by
Gordon Smyth
50k • written 9.7 years ago by
assaf www
▴ 140
0
votes
1
reply
1.3k
views
rsqlite for windows from fhcrc
Transcription
BiocInstaller
Transcription
BiocInstaller
updated 9.7 years ago by
Martin Morgan
25k • written 9.7 years ago by
Kasper Daniel Hansen
★ 6.5k
0
votes
0
replies
1.3k
views
Useful information about Ensembl release 76 mart databases
Transcription
zebrafish
Transcription
zebrafish
9.7 years ago
Thomas Maurel
▴ 800
0
votes
1
reply
1.7k
views
An. Gambie RNA-Seq differential expression using gage and pathview
Transcription
Annotation
Normalization
gage
pathview
Transcription
Annotation
Normalization
updated 9.8 years ago by
Saul Lozano
▴ 20 • written 9.8 years ago by
Luo Weijun
★ 1.6k
0
votes
0
replies
1.2k
views
An. Gambie RNA-Seq differential expression using gage and pathview
Transcription
Normalization
gage
Transcription
Normalization
gage
9.8 years ago
Saul Lozano
▴ 20
0
votes
4
replies
1.3k
views
Limma package and minimal number of genes
Transcription
limma
Transcription
limma
updated 9.9 years ago by
Paul Geeleher
★ 1.3k • written 9.9 years ago by
Bas van Gestel
▴ 10
0
votes
1
reply
1.2k
views
total count filter cutoff
Transcription
Transcription
updated 10.0 years ago by
Mahnaz Kiani
▴ 20 • written 10.0 years ago by
Wolfgang Huber
★ 13k
0
votes
1
reply
2.2k
views
Deseq2-help
Transcription
DESeq
DESeq2
Transcription
DESeq
DESeq2
updated 10.0 years ago by
Mubarak hussain Syed
▴ 30 • written 10.0 years ago by
Michael Love
41k
1
vote
0
replies
1.3k
views
question on MotifDb package
Transcription
MotifDb
Transcription
MotifDb
10.1 years ago
Paul Shannon
▴ 470
0
votes
7
replies
2.1k
views
Low number of replicates DESeq
Transcription
GO
DESeq2
Transcription
GO
DESeq2
updated 10.1 years ago by
Michael Love
41k • written 10.1 years ago by
Federico Gaiti
▴ 130
0
votes
0
replies
1.4k
views
questions related to DiffBind package
Transcription
Normalization
DiffBind
Transcription
Normalization
DiffBind
10.2 years ago
Rory Stark
★ 5.1k
0
votes
1
reply
1.6k
views
DiffBind loading Problem
Transcription
ChIPSeq
chipseq
DiffBind
Transcription
ChIPSeq
chipseq
DiffBind
10.2 years ago
Rory Stark
★ 5.1k
0
votes
4
replies
1.5k
views
Rcade analysis without ChIP-seq replicates
Transcription
Rcade
Transcription
Rcade
updated 10.2 years ago by
Jonathan Cairns
▴ 60 • written 10.2 years ago by
André Faure
▴ 30
0
votes
2
replies
2.2k
views
ensemblVEP, variant_effect_predictor versions and release schedule
Transcription
HapMap
PolyPhen
SIFT
convert
genomes
ensemblVEP
Transcription
HapMap
SIFT
updated 10.3 years ago by
Valerie Obenchain
★ 6.8k • written 10.3 years ago by
Thomas Sandmann
▴ 30
0
votes
1
reply
1.9k
views
Analysis of Affymetrix Human Gene 2.0 ST arrays
Transcription
Annotation
Normalization
GO
hgu133plus2
affy
PROcess
Category
Transcription
updated 10.4 years ago by
Federico Lasa
▴ 80 • written 10.4 years ago by
María Maqueda González
▴ 20
0
votes
0
replies
4.0k
views
Bioconductor 2.13 is released
BiocViews
aCGH
SNP
Transcription
Sequencing
miRNA
Microarray
Genetics
Proteomics
Coverage
10.5 years ago
Dan Tenenbaum
★ 8.2k
0
votes
0
replies
1.3k
views
DNaseR - a new Bioconductor package for DNase-seq digital genomic footprinting
Transcription
DNaseR
Transcription
DNaseR
10.5 years ago
Pedro Madrigal
▴ 20
0
votes
0
replies
3.0k
views
DiffBind questions
Transcription
Cancer
DiffBind
MMDiff
Transcription
Cancer
DiffBind
MMDiff
10.6 years ago
Rory Stark
★ 5.1k
0
votes
2
replies
3.7k
views
TranscriptDb of GENCODE Genes
Transcription
Annotation
Transcription
Annotation
updated 10.7 years ago by
Marc Carlson
★ 7.2k • written 10.7 years ago by
Dario Strbenac
★ 1.5k
1
vote
4
replies
1.5k
views
Is GO.db out of date?
Transcription
GO
Transcription
GO
11.1 years ago
chawla
▴ 190
0
votes
2
replies
1.2k
views
matchPWM() questions
Transcription
Transcription
updated 11.1 years ago by
Hervé Pagès
16k • written 11.1 years ago by
Ugo Borello
▴ 340
0
votes
0
replies
1.1k
views
BitSeq: Required input for 3' bias correction on transcripts.
Transcription
RNASeq
safe
BitSeq
Transcription
RNASeq
safe
BitSeq
11.2 years ago
Peter Glaus
▴ 70
0
votes
1
reply
1.7k
views
promoter prediction
Transcription
MotIV
MotifDb
Transcription
MotIV
MotifDb
updated 11.4 years ago by
Jing Huang
▴ 380 • written 11.4 years ago by
Paul Shannon
▴ 750
0
votes
0
replies
3.8k
views
ComBat
Transcription
Genetics
Pathways
Network
Survival
Cancer
Breast
Colon
Kidney
Leukemia
HIV
11.5 years ago
SSc Array Core
▴ 10
0
votes
0
replies
3.1k
views
Bioconductor 2.11 is released
BiocViews
SNP
Transcription
Sequencing
miRNA
Microbiome
Microarray
qPCR
Genetics
Coverage
11.5 years ago
Dan Tenenbaum
★ 8.2k
1
vote
5
replies
2.2k
views
paCalls oligo package
Transcription
oligo
Transcription
oligo
updated 11.6 years ago by
James W. MacDonald
65k • written 11.6 years ago by
Juan Fernández Tajes
▴ 190
0
votes
1
reply
1.8k
views
Bioconductor Digest, Vol 115, Issue 22
Transcription
Sequencing
miRNA
SmallRNA
Annotation
Normalization
GO
Cancer
Organism
edgeR
updated 11.6 years ago by
Steve Lianoglou
★ 13k • written 11.6 years ago by
Weng Khong LIM
▴ 10
0
votes
0
replies
1.3k
views
NGS public data analysis
Transcription
DEGseq
Transcription
DEGseq
11.6 years ago
Jill Pleasance
▴ 10
0
votes
1
reply
1.5k
views
Differential expression analysis of CAGE data
Transcription
Annotation
convert
edgeR
DESeq
Transcription
Annotation
convert
edgeR
DESeq
updated 11.6 years ago by
Steve Lianoglou
★ 13k • written 11.6 years ago by
Makis Motakis
▴ 30
0
votes
0
replies
918
views
ChIPpeakAnno - c elegans annotation feature type: translation start site
Transcription
Transcription
11.6 years ago
Julie Zhu
★ 4.3k
0
votes
4
replies
4.8k
views
GRanges DitancetoNearest query
Transcription
GenomicRanges
Transcription
GenomicRanges
updated 11.7 years ago by
Steve Lianoglou
★ 13k • written 11.7 years ago by
d r
▴ 150
0
votes
0
replies
935
views
GOstats adding custom annotations
Transcription
miRNA
GO
Transcription
miRNA
GO
11.7 years ago
sudeep s
▴ 60
0
votes
2
replies
1.8k
views
goTools: Error in goidvect[test] : invalid subscript type \'list\'
Transcription
Microarray
Annotation
GO
goTools
Transcription
Microarray
Annotation
GO
updated 11.8 years ago by
James W. MacDonald
65k • written 11.8 years ago by
Guest User
★ 13k
0
votes
4
replies
1.5k
views
AffyID mapping question
Transcription
mouse4302
Transcription
mouse4302
updated 11.8 years ago by
Marc Carlson
★ 7.2k • written 11.8 years ago by
Guest User
★ 13k
0
votes
11
replies
2.5k
views
"graphite" Biocarta 'native' graphs different from Biocarta web site?
Transcription
Pathways
Leukemia
graphite
Transcription
Pathways
Leukemia
graphite
11.9 years ago
Hamid Bolouri
▴ 90
0
votes
5
replies
1.5k
views
predicting transcription factors
Transcription
Transcription
updated 11.9 years ago by
Paul Shannon
▴ 750 • written 11.9 years ago by
Jing Huang
▴ 380
0
votes
0
replies
1.1k
views
Biological Pathway Database
Transcription
Pathways
Category
Transcription
Pathways
Category
12.0 years ago
Gita Singh
▴ 10
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Comment: Which input file is used for DGEList in EgdeR?
by
Michael Love
41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
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41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
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41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
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