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diffbind
•
reset
0
votes
2
replies
256
views
ATACseq rudimentary questions
ATACSeq
DiffBind
9 weeks ago • updated 8 weeks ago
4747
• 0
1
vote
11
replies
8.0k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
written 2.9 years ago by
Oscar
▴ 10
0
votes
1
reply
374
views
DiffBind plot.profile error
BiocParallel
DiffBind
written 9 months ago by
this_is_me_trying
• 0
0
votes
0
replies
1.2k
views
Diffbind Analysis gives error during profile plotting stage. Error in value[[3L]](cond) : profileplyr error: Error: BiocParallel errors 1 remote…
chipseq
profileplyr
DiffBind
9 months ago
Muhammad
• 0
0
votes
0
replies
459
views
I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap
mergingpeaks
ChIPseq
DiffBind
10 months ago
atlanta
• 0
0
votes
4
replies
2.5k
views
DiffBind can't find a DAR
dar
ATACSeq
DiffBind
11 months ago • updated 10 months ago
Mengjun
• 0
0
votes
0
replies
312
views
DiffBind multi-tissue comparison
DiffBind
11 months ago
lryrainche
• 0
1
vote
8
replies
3.0k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
11 months ago • updated 10 months ago
Luca
• 0
0
votes
0
replies
434
views
DiffBind recommendation on using IgG bams
peakcalling
DiffBind
12 months ago
Harish
• 0
0
votes
4
replies
1.6k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR
DiffBind
updated 12 months ago by
Harry
• 0 • written 12 months ago by
tifaGis
• 0
0
votes
1
reply
526
views
building samplesheet and plot profile
DiffBind
13 months ago
yf
• 0
0
votes
5
replies
1.0k
views
Diffbind interpretation of data - fold change
DiffBind
14 months ago • updated 13 months ago
Vera
• 0
0
votes
0
replies
841
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
16 months ago
kim
• 0
0
votes
0
replies
496
views
diffbind covariates
DiffBind
ATACSeq
updated 16 months ago by
Michael Love
43k • written 16 months ago by
Alpesh Querer
▴ 220
0
votes
2
replies
1.1k
views
DiffBind dba.report discrepancy
DiffBind
16 months ago
aelbassiouny
• 0
0
votes
0
replies
390
views
DiffBind subset replicates
DiffBind
16 months ago
Haiping
• 0
0
votes
0
replies
767
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
16 months ago
Young Boqin
• 0
0
votes
0
replies
589
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
17 months ago
Alejandro
• 0
0
votes
2
replies
721
views
DiffBind for MBD-seq
MBD-seq
DiffBind
18 months ago
Marianna
▴ 20
0
votes
1
reply
801
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
18 months ago • updated 12 months ago
Ian D.
▴ 70
0
votes
1
reply
689
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
18 months ago
mdidish
▴ 10
0
votes
0
replies
577
views
DiffBind dba.plotprofile y-axis range
DiffBind
18 months ago
Tara
• 0
0
votes
8
replies
1.5k
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 19 months ago by
Rory Stark
★ 5.3k • written 19 months ago by
Marianna
▴ 20
1
vote
3
replies
1.1k
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 19 months ago by
Rory Stark
★ 5.3k • written 19 months ago by
jesswhitts
• 0
0
votes
0
replies
915
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
20 months ago
gamma.jian
▴ 10
0
votes
2
replies
1.1k
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
20 months ago
Mallory
• 0
0
votes
0
replies
587
views
Difference in Contrast in DiffBind
DiffBind
21 months ago
user_bioinfo
• 0
0
votes
0
replies
571
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
22 months ago
Dinesh
• 0
0
votes
1
reply
1.2k
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 16 months ago by
B.N
• 0 • written 22 months ago by
Henry
▴ 10
0
votes
0
replies
913
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
22 months ago
yvonneh
• 0
0
votes
0
replies
548
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
22 months ago
Ian D.
▴ 70
0
votes
9
replies
2.1k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
22 months ago • updated 16 months ago
Ian D.
▴ 70
3
votes
1
reply
1.1k
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 22 months ago by
Michael Love
43k • written 22 months ago by
marcusn
▴ 10
0
votes
1
reply
1.7k
views
ATACseq merge peaks
DiffBind
updated 22 months ago by
ATpoint
★ 5.0k • written 22 months ago by
Shloka
• 0
0
votes
4
replies
1.0k
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
22 months ago
lonn
• 0
0
votes
0
replies
589
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
22 months ago
Virangika
• 0
2
votes
2
replies
1.2k
views
[DiffBind] Obtaining normalization factors
DiffBind
23 months ago • updated 22 months ago
Henry
▴ 10
2
votes
2
replies
2.2k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
23 months ago
Henry
▴ 10
0
votes
0
replies
700
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
23 months ago
feather-W
• 0
0
votes
0
replies
708
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
23 months ago
Ankit
▴ 20
0
votes
0
replies
731
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
23 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
631
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
23 months ago
erbrocato
• 0
0
votes
2
replies
1.0k
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
24 months ago • updated 23 months ago
Sam
▴ 10
0
votes
1
reply
877
views
Exact same results in Diffbind with different normalization methods
DiffBind
24 months ago • updated 23 months ago
red_bricks
▴ 60
0
votes
1
reply
1.2k
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
2.1 years ago
isaromero8888
• 0
0
votes
0
replies
1.1k
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
2.1 years ago
Jawahar
• 0
0
votes
0
replies
676
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
2.1 years ago
frueher
• 0
0
votes
0
replies
601
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
2.1 years ago
Aswathy
• 0
0
votes
0
replies
930
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
2.2 years ago
Hai
• 0
0
votes
0
replies
754
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
2.2 years ago
inna.gur
• 0
679 results • Page
1 of 14
Recent ...
Replies
Answer: GSEA error
by
James W. MacDonald
68k
At a very high level, the way non-model organisms are annotated is by using blast to find orthologs in other species that are well annotate…
Comment: Unable to find ENTREZ IDs
by
Adithi
• 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Comment: Unable to find ENTREZ IDs
by
Adithi
• 0
Hi James, Thank you so much for your reply. My main goal is to find ortholog genes from chinese hamster gene symbols to mouse gene symbols…
Answer: Unable to find ENTREZ IDs
by
James W. MacDonald
68k
Those are the 'symbols', and are a concatenation of LOC and the NCBI Gene ID (what used to be called an Entrez Gene ID). As an example:http…
Answer: Inconsistencies between accessor functions for TxDb databases with selected seql
by
a2a2hd42aa
• 0
Technical inconsistencies in database accessors can disrupt your workflow, but finding a reliable source to download online mobile games sh…
Votes
Answer: OrgDb for maize
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
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