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447 results • Page
1 of 9
Sort: Rank
Rank
Views
Votes
Replies
3
votes
4
replies
61
views
Help with running egsea()
EGSEA
13 minutes ago by
Chris
▴ 270
0
votes
1
reply
47
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 2 hours ago by
ATpoint
82k • written 2 hours ago by
ahmad.sajad4541
• 0
1
vote
4
replies
61
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
9 minutes ago by
Assa Yeroslaviz
★ 1.8k
0
votes
1
reply
62
views
student
epitranscriptomics
updated 2 hours ago by
ATpoint
82k • written 3 hours ago by
useriwa
• 0
0
votes
0
replies
37
views
Imputation of missing genotypes
panel
beagle
imputation
3 hours ago by
analyst
▴ 30
0
votes
3
replies
57
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 4 minutes ago by
GenoMax
142k • written 3 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
34
views
Correlation Analysis
statistics
methylation
NGS
expression
4 hours ago by
Researcher
▴ 30
1
vote
1
reply
58
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
updated 1 hour ago by
ATpoint
82k • written 4 hours ago by
robert.flynn.21
• 0
0
votes
0
replies
39
views
Gene density plot
density
gene
5 hours ago by
gubrins
▴ 290
1
vote
3
replies
106
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex
bwt
updated 4 hours ago by
Michael
54k • written 6 hours ago by
qwertyuiop26
• 0
0
votes
0
replies
65
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
17 hours ago by
Scott McKay
▴ 30
0
votes
0
replies
67
views
Cellphonedb results
cpdb
visulization
cellphonedb
18 hours ago by
piotto
▴ 20
0
votes
2
replies
141
views
Applying the metacell2 algorithm using python
single-cell
scanpy
cells
meta
python
2 hours ago by
JACKY
▴ 140
0
votes
0
replies
75
views
Cox Model with interaction item interpretation
Cox
23 hours ago by
Bine
▴ 60
0
votes
0
replies
66
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
23 hours ago by
Javier
• 0
1
vote
5
replies
339
views
Question regarding WGCNA
WGCNA
Network-construction
24 minutes ago by
deepak
• 0
0
votes
0
replies
75
views
vdjtools
vdjtools
1 day ago by
yueli7
▴ 250
0
votes
1
reply
121
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 3 hours ago by
andres.firrincieli
3.6k • written 1 day ago by
Antonio
• 0
0
votes
0
replies
86
views
Error while loading model of Spatial data deconvolution using cell2location
Python
cell2location
updated 1 day ago by
Ram
43k • written 1 day ago by
sidrah.maryam
▴ 50
0
votes
0
replies
75
views
Normalizing AMR gene count data
abundance
RGI
updated 1 day ago by
Ram
43k • written 1 day ago by
arshad1292
▴ 100
0
votes
0
replies
85
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
sarumonsus
• 0
0
votes
0
replies
93
views
How to implement an IGV to streamlit app?
python
streamlit
igv
1 day ago by
avigail.shnaider
• 0
0
votes
0
replies
108
views
Mitogenomes gap closure and making circular genome
gapclosure
Mitogenomes
validation
circulargenome
1 day ago by
KHURRAM SHAHZAD
• 0
0
votes
0
replies
105
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria
Metagenomics
Database
1 day ago by
Christopher
• 0
0
votes
0
replies
113
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
2 days ago by
DGTool
• 0
0
votes
0
replies
120
views
Seurat V5 integration
Seurat
samples
integration
combine
2 days ago by
starswillfade
▴ 10
0
votes
1
reply
171
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 18 hours ago by
bk11
★ 2.4k • written 2 days ago by
Yoosef
▴ 60
0
votes
1
reply
252
views
creating batch colum for batch correction
batch-correction
combat
1 day ago by
Expert
▴ 10
0
votes
1
reply
203
views
Help with DGEList function
DGEList
R
updated 1 day ago by
marco.barr
▴ 90 • written 3 days ago by
Natali
• 0
0
votes
0
replies
146
views
Homer motif analysis
Homer
3 days ago by
daffodil
▴ 10
0
votes
4
replies
270
views
HCL database download
database
HCL
human
updated 2 hours ago by
GenoMax
142k • written 3 days ago by
sooni
▴ 20
0
votes
1
reply
195
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Ximena
• 0
0
votes
1
reply
188
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 3 days ago by
Ram
43k • written 3 days ago by
Valentina
• 0
0
votes
6
replies
404
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 3 days ago by
swbarnes2
14k • written 4 days ago by
Erina
• 0
1
vote
3
replies
273
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
1 day ago by
Lada
▴ 30
1
vote
0
replies
144
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 1 day ago by
zx8754
11k • written 3 days ago by
Emilie
▴ 10
0
votes
0
replies
136
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
3 days ago by
Javier
• 0
0
votes
1
reply
229
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 3 days ago by
Thanujay S
• 0 • written 3 days ago by
yahn
• 0
0
votes
0
replies
129
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
3 days ago by
mikemakaveli1
• 0
2
votes
2
replies
212
views
Raw counts using stringtie
stringtie
RNA-seq
updated 3 days ago by
GenoMax
142k • written 4 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
129
views
Modify plot R mtDNA indel
plot
mtDNA
R
4 days ago by
marco.barr
▴ 90
0
votes
0
replies
280
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
4 days ago by
NorbertK
• 0
0
votes
2
replies
242
views
Downloading older version of a tool
Alignment
tools
3 days ago by
Ruqaiya
• 0
0
votes
0
replies
145
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
4 days ago by
rustykb
▴ 20
3
votes
5
replies
276
views
Generating mpileup file using samtools
mpileup
samtools
updated 4 days ago by
Joe
21k • written 4 days ago by
Ruqaiya
• 0
2
votes
3
replies
278
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 3 days ago by
dthorbur
★ 1.9k • written 4 days ago by
Vijith
▴ 30
0
votes
0
replies
145
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
4 days ago by
Jeyong
• 0
0
votes
0
replies
132
views
Empty table plot using plotGseaTable()
FGSEA
3 days ago by
Chris
▴ 270
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 4 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
195
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
4 days ago by
dtnondorf
• 0
447 results • Page
1 of 9
Recent Votes
Comment: Repeated testing/data mining in RNA Seq
Comment: UMI-Tools knee-method has great influence on the results of white list
A: LogFC and LogCPM
Comment: Help with running egsea()
removeBatchEffect explained using base R linear models
Comment: Help with running egsea()
Why employ normalization methods, and how can they be utilized in DEG analysis?
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Recent Awards •
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Darya
• 0
Popular Question
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Papyrus
★ 2.9k
Popular Question
to
hkarakurt
▴ 180
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GenoMax
142k
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anasjamshed
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Recent Replies
Comment: UMI-Tools knee-method has great influence on the results of white list
by
Assa Yeroslaviz
★ 1.8k
Thank you for the explanation. I can see the plots look strange, but i truly don't know why this is. I have a feeling that the sequencing …
Comment: High Malat-1 expression in single cell data
by
dsull
★ 6.0k
No -- those are ribosomal proteins, not rRNAs.
Comment: trying to count a pattern in my fastq file using bbduk
by
GenoMax
142k
Thanks for that link. As noted in that example, you can try `seal.sh` instead of `bbduk.sh`. > Is it possible, that this pattern is just …
Comment: Question regarding WGCNA
by
deepak
• 0
These are independent biological replicates
Comment: UMI-Tools knee-method has great influence on the results of white list
by
i.sudbery
19k
I didn't mean to sound like I was taking it as a criticism, I genuinely meant that we never intended to be a foolproof whitelisting tool. T…
Comment: Help with running egsea()
by
Chris
▴ 270
Thanks 1769mkc! I also tried fgsea. The author of limma comment on this post that p value from fgsea is not truly significant as it is http…
Comment: trying to count a pattern in my fastq file using bbduk
by
Assa Yeroslaviz
★ 1.8k
yes it does. As far as I understand it, you can use `N` here. I took it from [this example][1] Brian posted a few years ago This is why…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
Assa Yeroslaviz
★ 1.8k
thanks for the answer. I wasn't complaining about the tool (or the results for that matter). I'm just trying to understand why the differe…
Comment: Help with running egsea()
by
1769mkc
★ 1.2k
"c2 gene set from MSigDB." this i agree in that case https://bioconductor.org/packages/release/bioc/html/fgsea.html you can try this one wh…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
i.sudbery
19k
If you can post the knee plot, that might be helpful. But I will add that the whitelist command in UMI-tools was primarily designed to be a…
Comment: Help with running egsea()
by
Chris
▴ 270
Thanks 1769mkc! I tried this tool. Gene expression of 2 groups is just slightly different (not hundred of differential express genes). The …
Comment: Help with running egsea()
by
1769mkc
★ 1.2k
https://metascape.org/ this is one of the ways to make life easier if you have the genes already from the differential list
Comment: RNA editing sites based on DNA seq and RNA seq
by
Ahiad Chen Zion
• 0
In those unaligned reads, I am looking for hyper-editing. But the alignment should be much higher
Comment: Bacterial plasmid analysis
by
GenoMax
142k
Once you have some of these basic issues sorted out you can create a `tools` post describing `pling`.
Comment: Bacterial plasmid analysis
by
Daria
▴ 30
Hi, you need to run it with `PYTHONPATH=<pling_path>` in front of the command (a bit clunky, I know -- will likely be fixed in the next ver…
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