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
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
10
views
A question about reference genome for creating the consensus sequence
fasta
fa
cram
genome
50 minutes ago by
me
• 0
0
votes
0
replies
17
views
meffil.snp.concordance
meffil
methylation
snp_concordance
1 hour ago by
kyj222637
• 0
0
votes
0
replies
19
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
2 hours ago by
sooni
▴ 20
0
votes
0
replies
36
views
STAR aligner error
RNA-seq
STAR
slurm
updated 1 hour ago by
Ram
43k • written 4 hours ago by
M.
▴ 30
0
votes
0
replies
34
views
monocle 3-- Could not get node in small cluster
monocle3
5 hours ago by
synat.keam
▴ 100
0
votes
1
reply
71
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
updated 1 hour ago by
Ram
43k • written 6 hours ago by
Nicholas
• 0
0
votes
3
replies
169
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 6 hours ago by
Ram
43k • written 10 hours ago by
schmince
• 0
0
votes
1
reply
86
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 12 hours ago by
GenoMax
142k • written 12 hours ago by
Sony
▴ 10
5
votes
5
replies
207
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
1 hour ago by
Chris
▴ 280
0
votes
1
reply
95
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 14 hours ago by
ATpoint
82k • written 14 hours ago by
ahmad.sajad4541
• 0
1
vote
5
replies
162
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 12 hours ago by
i.sudbery
19k • written 14 hours ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
112
views
student
epitranscriptomics
updated 15 hours ago by
ATpoint
82k • written 15 hours ago by
useriwa
• 0
0
votes
0
replies
68
views
Imputation of missing genotypes
panel
beagle
imputation
15 hours ago by
analyst
▴ 30
0
votes
3
replies
130
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 12 hours ago by
GenoMax
142k • written 15 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
64
views
Correlation Analysis
statistics
methylation
NGS
expression
16 hours ago by
Researcher
▴ 30
1
vote
2
replies
135
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
10 hours ago by
robert.flynn.21
• 0
1
vote
1
reply
99
views
Gene density plot
density
gene
updated 11 hours ago by
dthorbur
★ 1.9k • written 17 hours ago by
gubrins
▴ 290
1
vote
4
replies
177
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex
bwt
4 hours ago by
qwertyuiop26
• 0
0
votes
0
replies
83
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
1 day ago by
Scott McKay
▴ 30
0
votes
0
replies
86
views
Cellphonedb results
cpdb
visulization
cellphonedb
1 day ago by
piotto
▴ 20
0
votes
0
replies
91
views
Cox Model with interaction item interpretation
Cox
1 day ago by
Bine
▴ 60
0
votes
0
replies
83
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
1 day ago by
Javier
• 0
1
vote
6
replies
410
views
Question regarding WGCNA
WGCNA
Network-construction
updated 11 hours ago by
andres.firrincieli
3.6k • written 4 days ago by
deepak
• 0
0
votes
0
replies
92
views
vdjtools
vdjtools
1 day ago by
yueli7
▴ 250
0
votes
1
reply
149
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 15 hours ago by
andres.firrincieli
3.6k • written 1 day ago by
Antonio
• 0
0
votes
0
replies
101
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
90
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
102
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
109
views
How to implement an IGV to streamlit app?
python
streamlit
igv
1 day ago by
avigail.shnaider
• 0
0
votes
0
replies
120
views
Mitogenomes gap closure and making circular genome
gapclosure
Mitogenomes
validation
circulargenome
2 days ago by
KHURRAM SHAHZAD
• 0
0
votes
0
replies
111
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria
Metagenomics
Database
2 days ago by
Christopher
• 0
0
votes
0
replies
114
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
2 days ago by
DGTool
• 0
0
votes
0
replies
122
views
Seurat V5 integration
Seurat
samples
integration
combine
2 days ago by
starswillfade
▴ 10
0
votes
1
reply
177
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 1 day ago by
bk11
★ 2.4k • written 2 days ago by
Yoosef
▴ 60
0
votes
1
reply
253
views
creating batch colum for batch correction
batch-correction
combat
1 day ago by
Expert
▴ 10
0
votes
1
reply
209
views
Help with DGEList function
DGEList
R
updated 2 days ago by
marco.barr
▴ 90 • written 3 days ago by
Natali
• 0
0
votes
0
replies
149
views
Homer motif analysis
Homer
3 days ago by
daffodil
▴ 10
0
votes
1
reply
196
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 3 days ago by
GenoMax
142k • written 4 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 4 days ago by
Valentina
• 0
0
votes
6
replies
415
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 4 days ago by
swbarnes2
14k • written 4 days ago by
Erina
• 0
1
vote
3
replies
275
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
2 days ago by
Lada
▴ 30
1
vote
0
replies
145
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 1 day ago by
zx8754
11k • written 4 days ago by
Emilie
▴ 10
0
votes
0
replies
136
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
4 days ago by
Javier
• 0
0
votes
1
reply
230
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 3 days ago by
Thanujay S
• 0 • written 4 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
4 days ago by
mikemakaveli1
• 0
2
votes
2
replies
215
views
Raw counts using stringtie
stringtie
RNA-seq
updated 4 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
304
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
245
views
Downloading older version of a tool
Alignment
tools
3 days ago by
Ruqaiya
• 0
0
votes
0
replies
146
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
4 days ago by
rustykb
▴ 20
1,000 results • Page
1 of 20
Recent Votes
Answer: Is therer any suggestions on mapping rate of WGBS data?
A: Download full list of SNPs and their coordinates in hg38
Answer: HCL database download
Answer: Tissue-specific DEG analysis with DEseq2
Answer: TFs and Gene databases
Answer: TFs and Gene databases
Comment: How to access TCGA samples that were treated with a specific drug?
Recent Locations •
All
South Korea,
7 minutes ago
Perth, Australia,
8 minutes ago
Australia,
9 minutes ago
Whitefish, MT,
14 minutes ago
United States,
16 minutes ago
Hong Kong,
16 minutes ago
Bologna,
16 minutes ago
Recent Awards •
All
Scholar
to
sooni
▴ 20
Teacher
to
jared.andrews07
★ 16k
Popular Question
to
synat.keam
▴ 100
Popular Question
to
bioinf_sci
▴ 20
Popular Question
to
hafiz.talhamalik
▴ 350
Popular Question
to
Maxine
▴ 40
Popular Question
to
jleehan
▴ 120
Recent Replies
Comment: Is therer any suggestions on mapping rate of WGBS data?
by
Zeng Jingyu
▴ 60
Thank you for your answer!
Answer: HCL database download
by
sooni
▴ 20
I solved the problem by conneting another internet exploer. I think it was probably a problem with Chrome itself.
Answer: barcode of TCR-sequencing
by
mizraelson
▴ 60
Hi, What protocol did you use for TCR-seq library preparation? Generally speaking, there is no need to remove barcodes, as MiXCR can work …
Comment: Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, C
by
qwertyuiop26
• 0
I've implemented fm index with backward search and need an inexact search to implement on FM index, I couldn't understand how fm index coul…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 400
The md5 hash they refer to on line 22 (f46a7ca244afef522b22a11bd33d27b1) appears to map to a *S. aureus* strain, not *S. hominis* (you can …
Comment: Correlating Bulk Differential Expression with quantitative
by
Qroid
▴ 40
You could try including disease scale for each sample as a design factor. See the vignette here https://bioconductor.org/packages/devel/bio…
Comment: Help with generating annotation database for dog genome to use in ANNOVAR for v
by
sainavyav22
• 0
Hello, Thanks for the reply. I could only see the refMrna.fa file in the link you provided. Where can I get the refGene.txt file. Thanks fo…
Answer: Understanding STAR output (Aligned.out.sam file)
by
heelpPlease
• 0
After thoroughly reviewing all the documents again, I've identified the root cause of my initial issue: the failure to detect essential gen…
Comment: Understanding STAR output (Aligned.out.sam file)
by
heelpPlease
• 0
Thank you! Now that I understand that there is a difference between read and fragment, I could actually find a lot of helpful information..…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
sovrappensiero
▴ 90
Thanks again. Hmm...this makes me suspicious of whether this normalization is actually possible. In case you'd like to take a look, [here]…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
Jeremy Leipzig
22k
The seven genotypes being 58025AA, 58025AG, 58051TT, 58051TC, 58051CC, 58057TT, 58057TC
Answer: TFs and Gene databases
by
jared.andrews07
★ 16k
See [TFlink](https://tflink.net/), [KnockTF2](https://bio.liclab.net/KnockTFv2/index.php), [TFBSDB](https://tfbsdb.systemsbiology.net/), an…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
GenoMax
142k
> Seven genotpyes have been sampled and all variants, which belong to one of those genotpyes are to be "erased" (or every other variant exc…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
Pierre Lindenbaum
161k
> , filter a multisample VCF file for all genotypes except one of them filter for what ?
Answer: Applying the metacell2 algorithm using python
by
Wayne
★ 2.0k
I had hoped things like [this Jupyter notebook for the rabbit data analysis](https://nbviewer.org/github/tanaylab/rabembflow/blob/master/2-…
Traffic: 1658 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