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13
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497
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Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
29 days ago • updated 26 days ago
fernanda.backsouza
▴ 10
0
votes
8
replies
398
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 26 days ago by
swbarnes2
★ 1.4k • written 27 days ago by
Aaliya
• 0
2
votes
7
replies
424
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
13 days ago • updated 10 days ago
sajadahmad41454
• 0
0
votes
3
replies
230
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 19 days ago by
ATpoint
★ 4.1k • written 19 days ago by
james.zhang20
• 0
0
votes
3
replies
200
views
ChAMP installation issue
Cha
ChAMP
8 days ago • updated 7 days ago
e1271094
• 0
1
vote
3
replies
895
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 27 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
0
votes
3
replies
117
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 3 days ago by
damian.szk
▴ 80 • written 3 days ago by
ninidea
• 0
0
votes
2
replies
268
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
28 days ago • updated 26 days ago
shuwangxinze1996
• 0
1
vote
2
replies
258
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
7 days ago • updated 4 days ago
BioinfGuru
▴ 30
0
votes
2
replies
114
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
7 days ago • updated 6 days ago
Yveto
• 0
0
votes
2
replies
740
views
Help with ENmix readidat
ENmix
IlluminaHumanMethylationEPICmanifest
updated 16 hours ago by
James W. MacDonald
66k • written 2.0 years ago by
Daphna
• 0
0
votes
1
reply
1.3k
views
DSS CpG coverage threshold
DSS
WGBS
coverage
updated 11 days ago by
j.gilbert
• 0 • written 6.6 years ago by
floriandeckert
▴ 30
0
votes
1
reply
41
views
ENCORI or starBase : ceRNA data retrieval using Web API and curl
curl
microRNA
starBase
webapi
ENCORI
updated 1 day ago by
ATpoint
★ 4.1k • written 1 day ago by
V_Vibes
• 0
0
votes
0
replies
15
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
5 days ago
oliverelijhan
0
0
votes
0
replies
97
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
18 days ago
yvonneh
• 0
0
votes
0
replies
98
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
26 days ago
Dario Strbenac
★ 1.5k
0
votes
0
replies
46
views
Difference in Contrast in DiffBind
DiffBind
6 days ago
zzrammal
• 0
0
votes
0
replies
89
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
5 days ago
Anton01
• 0
0
votes
0
replies
54
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
5 days ago
k200987
• 0
0
votes
0
replies
25
views
Processing of curatedmetagenomics
curatedMetagenomicData
1 day ago
Edward
• 0
0
votes
0
replies
61
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
5 days ago
Shaimaa Gamal
• 0
0
votes
0
replies
59
views
determine k during RUVSeq
RUVSeq
RUVnormalize
4 days ago
Ειρήνη
• 0
0
votes
0
replies
34
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq
scRNAseq
2 days ago
Bibi
• 0
0
votes
0
replies
54
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
5 days ago
danalvoronov
▴ 10
0
votes
0
replies
63
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
7 days ago
Researcher
• 0
0
votes
0
replies
89
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
18 days ago
Ian D.
▴ 70
0
votes
0
replies
21
views
Documenting resources in an `ExperimentHub` package?
AnnotationHub
ExperimentHub
12 hours ago
Tim Barry
• 0
0
votes
0
replies
98
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
21 days ago
Chris
▴ 10
0
votes
0
replies
101
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
26 days ago • updated 22 days ago
Sara
• 0
0
votes
0
replies
144
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
26 days ago • updated 18 days ago
glaciya2018
• 0
0
votes
0
replies
12
views
Spam:
Understanding Laser Hair Removal?
healthyControlsPresenceChecker
1 day ago
shahrozimmac
0
0
votes
0
replies
88
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
11 days ago
neilzhao
▴ 30
0
votes
0
replies
100
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
14 days ago
Dinesh
• 0
0
votes
0
replies
100
views
flowStats for CyTOF
flowStats
18 days ago
tholmes
• 0
0
votes
0
replies
142
views
Empty table plot using plotGseaTable()
fgsea
19 days ago • updated 17 days ago
Chris
▴ 10
0
votes
0
replies
78
views
Treeio as.treedata function seq lenght error
treeio
13 days ago
nromerov
• 0
0
votes
0
replies
47
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets
allele_freq
biomaRt
getBM
3 days ago • updated 2 days ago
Abiologist
• 0
0
votes
0
replies
125
views
dba.plotProfile() plotting and interpretation
DiffBind
17 days ago
Henry
▴ 10
38 results • Page
1 of 1
Recent ...
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Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Comment: Errors in chromosome annotation-biomaRt
by
blackwidowzzz
• 0
I recommend using a different dataset specific to your rat genome assembly version 8. You can search for available datasets within Ensembl …
Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
66k
In that case, probably easiest to subset to the groups being compared.
Votes
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Comment: DESeq2- Mysterious interaction suppresses DEGs
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