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diffBind
•
reset
1
vote
11
replies
6.8k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
written 2.5 years ago by
Oscar
▴ 10
0
votes
0
replies
214
views
DiffBind plot.profile error
BiocParallel
DiffBind
4 months ago
this_is_me_trying
• 0
0
votes
0
replies
1.0k
views
Diffbind Analysis gives error during profile plotting stage. Error in value[[3L]](cond) : profileplyr error: Error: BiocParallel errors 1 remote…
chipseq
profileplyr
DiffBind
5 months ago
Muhammad
• 0
0
votes
0
replies
328
views
I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap
mergingpeaks
ChIPseq
DiffBind
6 months ago
atlanta
• 0
0
votes
4
replies
2.3k
views
DiffBind can't find a DAR
dar
ATACSeq
DiffBind
6 months ago
Mengjun
• 0
0
votes
0
replies
212
views
DiffBind multi-tissue comparison
DiffBind
7 months ago
lryrainche
• 0
1
vote
8
replies
2.6k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
7 months ago • updated 6 months ago
Luca
• 0
0
votes
0
replies
328
views
DiffBind recommendation on using IgG bams
peakcalling
DiffBind
8 months ago
Harish
• 0
0
votes
4
replies
1.4k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR
DiffBind
updated 8 months ago by
Harry
• 0 • written 8 months ago by
tifaGis
• 0
0
votes
1
reply
344
views
building samplesheet and plot profile
DiffBind
9 months ago
yf
• 0
0
votes
5
replies
789
views
Diffbind interpretation of data - fold change
DiffBind
9 months ago
Vera
• 0
0
votes
0
replies
550
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
12 months ago
kim
• 0
0
votes
0
replies
358
views
diffbind covariates
DiffBind
ATACSeq
updated 12 months ago by
Michael Love
43k • written 12 months ago by
Alpesh Querer
▴ 220
0
votes
2
replies
931
views
DiffBind dba.report discrepancy
DiffBind
12 months ago
aelbassiouny
• 0
0
votes
0
replies
315
views
DiffBind subset replicates
DiffBind
12 months ago
Haiping
• 0
0
votes
0
replies
569
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
12 months ago
Young Boqin
• 0
0
votes
0
replies
478
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
13 months ago
Alejandro
• 0
0
votes
2
replies
609
views
DiffBind for MBD-seq
MBD-seq
DiffBind
14 months ago
Marianna
▴ 20
0
votes
1
reply
696
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
14 months ago • updated 8 months ago
Ian D.
▴ 70
0
votes
1
reply
583
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
14 months ago
mdidish
▴ 10
0
votes
0
replies
489
views
DiffBind dba.plotprofile y-axis range
DiffBind
14 months ago
Tara
• 0
0
votes
8
replies
1.3k
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 14 months ago by
Rory Stark
★ 5.2k • written 15 months ago by
Marianna
▴ 20
1
vote
3
replies
887
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 15 months ago by
Rory Stark
★ 5.2k • written 15 months ago by
jesswhitts
• 0
0
votes
0
replies
711
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
16 months ago
gamma.jian
▴ 10
0
votes
2
replies
920
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
16 months ago
Mallory
• 0
0
votes
0
replies
489
views
Difference in Contrast in DiffBind
DiffBind
17 months ago
user_bioinfo
• 0
0
votes
0
replies
500
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
18 months ago
Dinesh
• 0
0
votes
1
reply
1.0k
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 11 months ago by
B.N
• 0 • written 18 months ago by
Henry
▴ 10
0
votes
0
replies
760
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
18 months ago
yvonneh
• 0
0
votes
0
replies
455
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
18 months ago
Ian D.
▴ 70
0
votes
9
replies
1.8k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
18 months ago • updated 12 months ago
Ian D.
▴ 70
3
votes
1
reply
858
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 18 months ago by
Michael Love
43k • written 18 months ago by
marcusn
▴ 10
0
votes
1
reply
1.3k
views
ATACseq merge peaks
DiffBind
updated 18 months ago by
ATpoint
★ 5.0k • written 18 months ago by
Shloka
• 0
0
votes
4
replies
926
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
18 months ago
lonn
• 0
0
votes
0
replies
510
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
18 months ago
Virangika
• 0
2
votes
2
replies
1.0k
views
[DiffBind] Obtaining normalization factors
DiffBind
18 months ago
Henry
▴ 10
2
votes
2
replies
1.7k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
18 months ago
Henry
▴ 10
0
votes
0
replies
596
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
19 months ago
feather-W
• 0
0
votes
0
replies
615
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
19 months ago
Ankit
▴ 20
0
votes
0
replies
587
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
19 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
561
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
19 months ago
erbrocato
• 0
0
votes
2
replies
896
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
19 months ago
Sam
▴ 10
0
votes
1
reply
743
views
Exact same results in Diffbind with different normalization methods
DiffBind
19 months ago
red_bricks
▴ 60
0
votes
1
reply
984
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
21 months ago
isaromero8888
• 0
0
votes
0
replies
921
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
21 months ago
Jawahar
• 0
0
votes
0
replies
575
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
21 months ago
frueher
• 0
0
votes
0
replies
533
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
21 months ago
Aswathy
• 0
0
votes
0
replies
770
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
22 months ago
Hai
• 0
0
votes
0
replies
656
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
22 months ago
inna.gur
• 0
2
votes
2
replies
2.0k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 6 months ago by
etiennedanis
• 0 • written 2.2 years ago by
Mark
▴ 10
678 results • Page
1 of 14
Recent ...
Replies
Comment: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated
by
shepherl
4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts
by
Michael Love
43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts
by
empty_mt
• 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts
by
Michael Love
43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Votes
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
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