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116,778 results • Page
2 of 2336
Sort: Rank
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Views
Votes
Replies
0
votes
0
replies
243
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
3 days ago by
NorbertK
• 0
2
votes
2
replies
217
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 1 day ago by
Ram
43k • written 3 days ago by
carolofharvest
▴ 30
9
votes
10
replies
589
views
High Malat-1 expression in single cell data
single-cell
updated 3 hours ago by
t.montserrat.ayuso
▴ 10 • written 7 days ago by
carolofharvest
▴ 30
0
votes
2
replies
237
views
Downloading older version of a tool
Alignment
tools
2 days ago by
Ruqaiya
• 0
0
votes
0
replies
144
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
3 days ago by
rustykb
▴ 20
1
vote
1
reply
177
views
DSEQ2 analysis
DESEQ2
logfoldchange
updated 1 day ago by
Ram
43k • written 3 days ago by
adi.gershon1
• 0
3
votes
5
replies
267
views
Generating mpileup file using samtools
mpileup
samtools
updated 3 days ago by
Joe
21k • written 3 days ago by
Ruqaiya
• 0
0
votes
5
replies
342
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 3 days ago by
b.contreras.moreira
▴ 180 • written 4 days ago by
JH
• 0
1
vote
3
replies
280
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 3 days ago by
ATpoint
82k • written 3 days ago by
Qi
• 0
0
votes
0
replies
135
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
3 days ago by
Amos Bairoch
▴ 120
2
votes
3
replies
273
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 2 days ago by
dthorbur
★ 1.9k • written 3 days ago by
Vijith
▴ 30
0
votes
0
replies
144
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
3 days ago by
Jeyong
• 0
0
votes
2
replies
727
views
homer not configured properly
Homer
makeTagDirectory
updated 3 days ago by
clairechung112
• 0 • written 23 months ago by
amahdi779
• 0
1
vote
3
replies
251
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 3 days ago by
Alex Reynolds
35k • written 3 days ago by
SJP
• 0
0
votes
0
replies
132
views
Empty table plot using plotGseaTable()
FGSEA
2 days ago by
Chris
▴ 260
0
votes
1
reply
179
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 3 days ago by
anovak
▴ 120 • written 3 days ago by
Hang
• 0
1
vote
3
replies
234
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 3 days ago by
jared.andrews07
★ 16k • written 3 days ago by
yvonneh
▴ 10
3
votes
5
replies
310
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
2 days ago by
Maverick
▴ 10
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 3 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
190
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
3 days ago by
dtnondorf
• 0
0
votes
1
reply
212
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 3 days ago by
Chris Dean
▴ 390 • written 3 days ago by
sovrappensiero
▴ 90
1
vote
2
replies
235
views
RNA-seq data for deep learning classification
rna-seq
3 days ago by
yahn
• 0
2
votes
7
replies
425
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
updated 1 day ago by
Zhenyu Zhang
★ 1.2k • written 3 days ago by
Qroid
▴ 40
0
votes
1
reply
509
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 3 days ago by
Hugo
• 0 • written 4 months ago by
Rachel
• 0
0
votes
1
reply
148
views
Provean help
variant
Provean
updated 3 days ago by
Mensur Dlakic
★ 27k • written 3 days ago by
Arun Sai Kumar
• 0
1
vote
1
reply
162
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated 3 days ago by
bk11
★ 2.4k • written 4 days ago by
Jeol
▴ 20
1
vote
1
reply
170
views
Super ehancers
enhancers
updated 3 days ago by
jared.andrews07
★ 16k • written 4 days ago by
Oburah
• 0
0
votes
6
replies
288
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
updated 2 days ago by
dsull
★ 6.0k • written 4 days ago by
Chen
• 0
5
votes
5
replies
273
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 4 days ago by
atharvakarkare14
▴ 30 • written 4 days ago by
Begonia_pavonina
▴ 150
1
vote
7
replies
439
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
3 days ago by
eebloom
▴ 80
3
votes
3
replies
315
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression
RNA
NOISeq
DGE
updated 3 days ago by
ATpoint
82k • written 4 days ago by
alifafiq1
• 0
0
votes
0
replies
100
views
Use of annotation of integrated Seurat object in single sample
Seurat
4 days ago by
Bine
▴ 60
0
votes
0
replies
105
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 3 days ago by
Ram
43k • written 4 days ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
223
views
Subsetting and merging back Seurat Object brings different results
Seurat
4 days ago by
Bine
▴ 60
0
votes
0
replies
138
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
NGS
Genomics
Post-doc
R-loops
updated 3 days ago by
Ram
43k • written 4 days ago by
4r-rtg
• 0
1
vote
1
reply
138
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 3 days ago by
Ram
43k • written 4 days ago by
marco.barr
▴ 90
0
votes
0
replies
96
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
4 days ago by
Vijith
▴ 30
9
votes
10
replies
505
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 3 days ago by
Zamin Iqbal
▴ 20 • written 4 days ago by
nicole.kavanagh
• 0
0
votes
1
reply
275
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 4 days ago by
Scooter
▴ 280 • written 10 days ago by
avocado123
• 0
0
votes
0
replies
96
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
4 days ago by
James
▴ 10
0
votes
1
reply
585
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 4 days ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
1
vote
3
replies
235
views
Odd alignment question/finding
Alignment
updated 3 days ago by
barslmn
★ 2.1k • written 4 days ago by
poordumbsillyidiot
• 0
0
votes
1
reply
206
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 4 days ago by
GenoMax
142k • written 4 days ago by
mgranada3
▴ 30
0
votes
0
replies
98
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
4 days ago by
meck
• 0
0
votes
0
replies
124
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 4 days ago by
Ram
43k • written 4 days ago by
Oscar
▴ 10
0
votes
7
replies
546
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 3 days ago by
LChart
3.9k • written 6 days ago by
kl
▴ 10
0
votes
1
reply
221
views
How to find overlap of clusters in two seurat porject
clustering
seurat
updated 4 days ago by
Adam
▴ 30 • written 5 days ago by
J
• 0
1
vote
3
replies
307
views
DESeq2 processing problems
deseq2
R
updated 4 days ago by
ATpoint
82k • written 5 days ago by
jagdish7921
• 0
0
votes
1
reply
781
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 3 days ago by
Ram
43k • written 2.7 years ago by
carov
• 0
0
votes
1
reply
151
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 4 days ago by
Ram
43k • written 4 days ago by
ernestine.kubi
• 0
116,778 results • Page
2 of 2336
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Answer: Quetion regarding WGCNA
by
deepak180001
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Thank you for your reply andres.firrincieli. I have attached the PCA plot of the expression data used in the WGCNA. ![enter imag…
Comment: Design matrix Differential expression analysis
by
SHN
▴ 40
Got it, thank you for your response. SN
Comment: How to interpret DEXseq results in therms of significance
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Hi, I used write.table(as.data.frame(DEXSeqResults(MyObj)), "Results.tsv", quote=FALSE, sep="\t", dec=".") to save the result but I recei…
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Can I ask what do you exactly mean by same experiment? If you are talking about the same donor and the same procedure, unfortunately, not a…
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Find someone with computer skills near you and consult them. From your posts on the forum, it's clear that you need help at a level that we…
Comment: Gene Specific coverage from WGS data
by
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142k
This is not going to work no matter what program you use since the chromosome identifiers in your GTF (`MN908947.3 `) do not match your BA…
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43k
Read the answers in the post, understand them and try to implement them.
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Just using the normalized expression of Malat1 works.
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Awesome, thank you for the concise and straight-forward answer!
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82k
Look, before you keep posting these sorts of questions and might gross of users, please read and follow https://www.biostars.org/p/357878/ …
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"Also if is there any other quick way to find gene specific coverage" can you give some example so that its bit more clear what do you mean…
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I am facing the same problem and I don't know how to solve the problem,....
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[How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning?](https://stackoverflow.com/q/25721884/680068)
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82k
Welcome to this community. Please learn the most important lesson right away which is reading answers and learning from it. Users gave you …
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