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42 results • Page
1 of 1
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
30
views
A question about reference genome for creating the consensus sequence
fasta
fa
cram
genome
3 hours ago by
me
• 0
0
votes
0
replies
32
views
meffil.snp.concordance
meffil
methylation
snp_concordance
4 hours ago by
kyj222637
• 0
0
votes
0
replies
29
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
4 hours ago by
sooni
▴ 20
1
vote
5
replies
331
views
HCL database download
HCL
updated 3 hours ago by
Ram
43k • written 4 days ago by
sooni
▴ 20
0
votes
1
reply
182
views
barcode of TCR-sequencing
barcode
updated 6 hours ago by
mizraelson
▴ 60 • written 7 days ago by
yueli7
▴ 250
0
votes
1
reply
52
views
STAR aligner error
RNA-seq
STAR
slurm
updated 20 minutes ago by
Ram
43k • written 7 hours ago by
M.
▴ 30
0
votes
0
replies
41
views
monocle 3-- Could not get node in small cluster
monocle3
7 hours ago by
synat.keam
▴ 100
0
votes
1
reply
81
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
updated 3 hours ago by
Ram
43k • written 8 hours ago by
Nicholas
• 0
1
vote
4
replies
282
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
10 hours ago by
heelpPlease
• 0
5
votes
1
reply
115
views
TFs and Gene databases
Transcription-factor
Target
Regulatory-Networks
updated 9 hours ago by
Ram
43k • written 12 hours ago by
ijarne
• 0
0
votes
5
replies
290
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 9 hours ago by
Ram
43k • written 1 day ago by
JACKY
▴ 140
0
votes
3
replies
186
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 9 hours ago by
Ram
43k • written 13 hours ago by
schmince
• 0
0
votes
0
replies
61
views
News:
Online course. -Time series analysis and Forecasting in R
Time-Series
Forecasting
R
Stastics
14 hours ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
410
views
HLA-HD tool for genomic imputation
genomics
imputation
bash
updated 7 hours ago by
Javier
• 0 • written 3 months ago by
fra.r.silvestro
▴ 10
0
votes
1
reply
91
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 14 hours ago by
GenoMax
142k • written 14 hours ago by
Sony
▴ 10
5
votes
5
replies
214
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
2 hours ago by
Chris
▴ 280
0
votes
1
reply
99
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 16 hours ago by
ATpoint
82k • written 17 hours ago by
ahmad.sajad4541
• 0
1
vote
5
replies
166
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 14 hours ago by
i.sudbery
19k • written 17 hours ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
117
views
student
epitranscriptomics
updated 17 hours ago by
ATpoint
82k • written 18 hours ago by
useriwa
• 0
0
votes
0
replies
73
views
Imputation of missing genotypes
panel
beagle
imputation
18 hours ago by
analyst
▴ 30
0
votes
3
replies
134
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 14 hours ago by
GenoMax
142k • written 18 hours ago by
Assa Yeroslaviz
★ 1.8k
5
votes
1
reply
108
views
Tutorial:
removeBatchEffect explained using base R linear models
limma
effects
batch
removebatcheffects
updated 18 hours ago by
dariober
14k • written 18 hours ago by
nhaus
▴ 340
2
votes
2
replies
104
views
Is therer any suggestions on mapping rate of WGBS data?
mapping
read
alignment
WGBS
2 hours ago by
Zeng Jingyu
▴ 60
1
vote
2
replies
209
views
News:
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering
Spatial-transcriptomics
updated 18 hours ago by
Weiwen
• 0 • written 1 day ago by
MICOS
▴ 10
0
votes
0
replies
67
views
Correlation Analysis
statistics
methylation
NGS
expression
19 hours ago by
Researcher
▴ 30
1
vote
2
replies
141
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
13 hours ago by
robert.flynn.21
• 0
1
vote
1
reply
183
views
Tool:
Converting Nebula Genomics Data to 23andMe Format
23andMe
Nebula
updated 16 hours ago by
Michael
54k • written 1 day ago by
Guillermo
• 0
1
vote
1
reply
102
views
Gene density plot
density
gene
updated 13 hours ago by
dthorbur
★ 1.9k • written 19 hours ago by
gubrins
▴ 290
1
vote
4
replies
196
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex
bwt
6 hours ago by
qwertyuiop26
• 0
0
votes
1
reply
134
views
What is the proper way to identify the cell types of scRNAseq cluster?
scRNAseq
updated 22 hours ago by
ATpoint
82k • written 1 day ago by
MAPK2
▴ 40
0
votes
3
replies
200
views
How to compute TPM normalized values for TCGA miRNA data?
TCGA
normalization
TPM
miRNA
updated 22 hours ago by
swbarnes2
14k • written 1 day ago by
Ngrin
• 0
1
vote
6
replies
414
views
Question regarding WGCNA
WGCNA
Network-construction
updated 14 hours ago by
andres.firrincieli
3.6k • written 4 days ago by
deepak
• 0
0
votes
1
reply
164
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 18 hours ago by
andres.firrincieli
3.6k • written 1 day ago by
Antonio
• 0
12
votes
13
replies
728
views
High Malat-1 expression in single cell data
single-cell
updated 14 hours ago by
dsull
★ 6.0k • written 8 days ago by
carolofharvest
▴ 30
1
vote
7
replies
488
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 8 hours ago by
Chris Dean
▴ 400 • written 5 days ago by
sovrappensiero
▴ 90
10
votes
14
replies
633
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 16 hours ago by
GenoMax
142k • written 6 days ago by
nicole.kavanagh
• 0
0
votes
2
replies
228
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
16 hours ago by
Ahiad Chen Zion
• 0
3
votes
3
replies
223
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
23 hours ago by
Adyasha
• 0
0
votes
4
replies
371
views
Highest variable features in single cell data
single-cell
18 hours ago by
carolofharvest
▴ 30
0
votes
2
replies
234
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
8 hours ago by
sainavyav22
• 0
2
votes
4
replies
709
views
Count all variants from vcf file
variants
vcf
Count
updated 20 hours ago by
Pierre Lindenbaum
161k • written 20 months ago by
t.ali
• 0
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 20 hours ago by
Pierre Lindenbaum
161k • written 5.7 years ago by
mostafarafiepour
▴ 180
42 results • Page
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Recent Votes
Answer: ChIP-seq datasets: input samples omitted?
Answer: ChIP-seq datasets: input samples omitted?
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
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Comment: STAR aligner error
by
Ram
43k
Talk to your HPC sysadmin - array jobs might be getting different kinds of nodes compared to standalone jobs.
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 ?
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