Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : all time
all time
today
this week
this month
this year
1,000 results • Page
3 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
128
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
10 days ago by
Omics data mining
▴ 260
0
votes
2
replies
190
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
10 days ago by
njornet
▴ 20
0
votes
2
replies
219
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 10 days ago by
Adam
▴ 30 • written 10 days ago by
Darya
• 0
0
votes
5
replies
286
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 10 days ago by
Joe
21k • written 10 days ago by
Lemonhope
• 0
0
votes
0
replies
182
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
9 days ago by
Winter
• 0
0
votes
0
replies
108
views
meffil.snp.concordance
meffil
methylation
snp_concordance
11 days ago by
kyj222637
• 0
0
votes
1
reply
165
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 10 days ago by
Bastien Hervé
5.3k • written 11 days ago by
sooni
▴ 20
1
vote
3
replies
264
views
STAR aligner error
RNA-seq
STAR
slurm
updated 10 days ago by
Ram
43k • written 11 days ago by
M.
▴ 30
0
votes
0
replies
102
views
monocle 3-- Could not get node in small cluster
monocle3
11 days ago by
synat.keam
▴ 100
0
votes
2
replies
221
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
10 days ago by
Nicholas
• 0
0
votes
1
reply
267
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 11 days ago by
GenoMax
142k • written 11 days ago by
Sony
▴ 10
5
votes
5
replies
323
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
10 days ago by
Chris
▴ 280
0
votes
2
replies
235
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 10 days ago by
swbarnes2
14k • written 11 days ago by
ahmad.sajad4541
• 0
1
vote
9
replies
405
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 8 days ago by
i.sudbery
19k • written 11 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
176
views
student
epitranscriptomics
updated 11 days ago by
ATpoint
82k • written 11 days ago by
useriwa
• 0
0
votes
3
replies
194
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 11 days ago by
GenoMax
142k • written 11 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
4
replies
310
views
Correlation Analysis
statistics
methylation
NGS
expression
7 days ago by
Researcher
▴ 30
1
vote
2
replies
194
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
11 days ago by
robert.flynn.21
• 0
0
votes
0
replies
123
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
12 days ago by
Scott McKay
▴ 30
0
votes
0
replies
110
views
Cellphonedb results
cpdb
visulization
cellphonedb
12 days ago by
piotto
▴ 20
0
votes
0
replies
121
views
Cox Model with interaction item interpretation
Cox
12 days ago by
Bine
▴ 60
0
votes
0
replies
110
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
9 days ago by
Javier
• 0
1
vote
7
replies
545
views
Question regarding WGCNA
WGCNA
Network-construction
9 days ago by
deepak
• 0
0
votes
0
replies
110
views
vdjtools
vdjtools
12 days ago by
yueli7
▴ 250
0
votes
1
reply
301
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 11 days ago by
andres.firrincieli
3.6k • written 12 days ago by
Antonio
• 0
0
votes
0
replies
123
views
Error while loading model of Spatial data deconvolution using cell2location
Python
cell2location
updated 12 days ago by
Ram
43k • written 12 days ago by
sidrah.maryam
▴ 50
0
votes
0
replies
107
views
Normalizing AMR gene count data
abundance
RGI
updated 12 days ago by
Ram
43k • written 12 days ago by
arshad1292
▴ 100
1
vote
1
reply
185
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 2 days ago by
Jordan M Eizenga
▴ 460 • written 12 days ago by
sarumonsus
▴ 10
0
votes
0
replies
126
views
How to implement an IGV to streamlit app?
python
streamlit
igv
12 days ago by
avigail.shnaider
• 0
0
votes
0
replies
136
views
Mitogenomes gap closure and making circular genome
gapclosure
Mitogenomes
validation
circulargenome
13 days ago by
KHURRAM SHAHZAD
• 0
0
votes
0
replies
126
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria
Metagenomics
Database
13 days ago by
Christopher
• 0
0
votes
0
replies
130
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
13 days ago by
DGTool
▴ 20
2
votes
3
replies
342
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 9 days ago by
bk11
★ 2.5k • written 13 days ago by
Yoosef
▴ 60
0
votes
1
reply
282
views
creating batch colum for batch correction
batch-correction
combat
12 days ago by
Expert
▴ 10
0
votes
1
reply
245
views
Help with DGEList function
DGEList
R
updated 13 days ago by
marco.barr
▴ 130 • written 14 days ago by
Natali
• 0
0
votes
0
replies
170
views
Homer motif analysis
Homer
14 days ago by
daffodil
▴ 10
0
votes
2
replies
278
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 8 days ago by
GenoMax
142k • written 15 days ago by
Ximena
• 0
0
votes
1
reply
221
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 14 days ago by
Ram
43k • written 15 days ago by
Valentina
• 0
0
votes
6
replies
490
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 15 days ago by
swbarnes2
14k • written 15 days ago by
Erina
• 0
1
vote
3
replies
342
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
13 days ago by
Lada
▴ 30
1
vote
0
replies
159
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 12 days ago by
zx8754
11k • written 15 days ago by
Emilie
▴ 10
0
votes
0
replies
147
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
15 days ago by
Javier
• 0
0
votes
2
replies
308
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 6 days ago by
Zhenyu Zhang
★ 1.2k • written 15 days ago by
yahn
• 0
0
votes
0
replies
139
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
15 days ago by
mikemakaveli1
• 0
2
votes
2
replies
251
views
Raw counts using stringtie
stringtie
RNA-seq
updated 15 days ago by
GenoMax
142k • written 15 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
137
views
Modify plot R mtDNA indel
plot
mtDNA
R
15 days ago by
marco.barr
▴ 130
0
votes
0
replies
336
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
15 days ago by
NorbertK
▴ 10
0
votes
2
replies
288
views
Downloading older version of a tool
Alignment
tools
14 days ago by
Ruqaiya
• 0
0
votes
0
replies
161
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
15 days ago by
rustykb
▴ 20
3
votes
5
replies
347
views
Generating mpileup file using samtools
mpileup
samtools
updated 15 days ago by
Joe
21k • written 15 days ago by
Ruqaiya
• 0
1,000 results • Page
3 of 20
Recent Votes
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
Recent Locations •
All
United States,
12 minutes ago
United States,
13 minutes ago
United States,
20 minutes ago
USA,
23 minutes ago
United States,
23 minutes ago
United States,
25 minutes ago
Hong Kong,
36 minutes ago
Recent Awards •
All
Popular Question
to
synat.keam
▴ 100
Scholar
to
jv
★ 1.8k
Popular Question
to
syedahamdani94
• 0
Popular Question
to
mohammadhassanj
▴ 260
Scholar
to
dsull
★ 6.0k
Popular Question
to
finswimmer
16k
Popular Question
to
Ezequiel
• 0
Recent Replies
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
by
anton.i.petrov
• 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Traffic: 1350 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6