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87 results • Page
1 of 2
Sort: Votes
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Views
Votes
Replies
5
votes
5
replies
213
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
1 hour ago by
Chris
▴ 280
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 1 day ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 5 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
3
votes
5
replies
278
views
Generating mpileup file using samtools
mpileup
samtools
updated 4 days ago by
Joe
21k • written 4 days ago by
Ruqaiya
• 0
3
votes
3
replies
223
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
22 hours ago by
Adyasha
• 0
3
votes
8
replies
506
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
1 day ago by
Qroid
▴ 40
2
votes
2
replies
1.8k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR
statistical test
parametric
non-parametric
updated 4 days ago by
e.r.zakiev
▴ 210 • written 3.8 years ago by
n.anuragsharma
▴ 40
2
votes
2
replies
2.6k
views
Pindel Segmentation Fault Error
pindel
updated 3 days ago by
Ruqaiya
• 0 • written 10.2 years ago by
Yuelin
▴ 20
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
2
votes
3
replies
282
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 4 days ago by
dthorbur
★ 1.9k • written 4 days ago by
Vijith
▴ 30
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
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
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 7 hours ago by
Chris Dean
▴ 400 • written 5 days ago by
sovrappensiero
▴ 90
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
1
vote
6
replies
352
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 4 days ago by
GenoMax
142k • written 22 days ago by
eebloom
▴ 80
1
vote
2
replies
231
views
Downloading full alignments from Pfam
pfam
2 days ago by
bef1
• 0
1
vote
2
replies
254
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
6 days ago by
rianna.collins
• 0
1
vote
3
replies
275
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
2 days ago by
Lada
▴ 30
1
vote
3
replies
241
views
Odd alignment question/finding
Alignment
updated 4 days ago by
barslmn
★ 2.1k • written 6 days ago by
poordumbsillyidiot
• 0
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
1
vote
1
reply
117
views
student
epitranscriptomics
updated 17 hours ago by
ATpoint
82k • written 18 hours ago by
useriwa
• 0
1
vote
2
replies
294
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
6 days ago by
Nafi
• 0
1
vote
14
replies
2.4k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 5 days ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
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
142
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 5 days ago by
Ram
43k • written 5 days ago by
marco.barr
▴ 90
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
231
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
150
views
Homer motif analysis
Homer
3 days ago by
daffodil
▴ 10
0
votes
0
replies
122
views
Seurat V5 integration
Seurat
samples
integration
combine
2 days ago by
starswillfade
▴ 10
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
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
120
views
Mitogenomes gap closure and making circular genome
gapclosure
Mitogenomes
validation
circulargenome
2 days ago by
KHURRAM SHAHZAD
• 0
0
votes
1
reply
210
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
111
views
How to implement an IGV to streamlit app?
python
streamlit
igv
1 day ago by
avigail.shnaider
• 0
0
votes
0
replies
106
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
1
reply
254
views
creating batch colum for batch correction
batch-correction
combat
1 day ago by
Expert
▴ 10
0
votes
0
replies
106
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
94
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
95
views
vdjtools
vdjtools
1 day ago by
yueli7
▴ 250
0
votes
0
replies
85
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
1 day ago by
Javier
• 0
0
votes
0
replies
93
views
Cox Model with interaction item interpretation
Cox
1 day ago by
Bine
▴ 60
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
0
replies
88
views
Cellphonedb results
cpdb
visulization
cellphonedb
1 day ago by
piotto
▴ 20
0
votes
0
replies
86
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
1 day ago by
Scott McKay
▴ 30
0
votes
0
replies
178
views
CellPhoneDB results
cellphonedb
cpdb
cell_surface_proteins
updated 1 day ago by
GenoMax
142k • written 10 weeks ago by
piotto
▴ 20
0
votes
0
replies
67
views
Correlation Analysis
statistics
methylation
NGS
expression
19 hours ago by
Researcher
▴ 30
0
votes
4
replies
371
views
Highest variable features in single cell data
single-cell
18 hours ago by
carolofharvest
▴ 30
0
votes
0
replies
73
views
Imputation of missing genotypes
panel
beagle
imputation
18 hours ago by
analyst
▴ 30
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
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
87 results • Page
1 of 2
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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