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449 results • Page
1 of 9
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
14
views
STAR aligner error
STAR
alignment
slurm
RNAseq
mapping
1 hour ago by
M.
▴ 30
0
votes
0
replies
16
views
monocle 3-- Could not get node in small cluster
monocle3
2 hours ago by
synat.keam
▴ 100
0
votes
1
reply
49
views
Correlating Bulk Differential Expression with quantitative
Expression
Differential
DESeq2
updated 2 hours ago by
Qroid
▴ 40 • written 2 hours ago by
Nicholas
• 0
0
votes
3
replies
133
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 3 hours ago by
Ram
43k • written 7 hours ago by
schmince
• 0
0
votes
1
reply
78
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 8 hours ago by
GenoMax
142k • written 8 hours ago by
Sony
▴ 10
5
votes
5
replies
190
views
Help with running egsea()
EGSEA
2 hours ago by
Chris
▴ 280
0
votes
1
reply
88
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 11 hours ago by
ATpoint
82k • written 11 hours ago by
ahmad.sajad4541
• 0
1
vote
5
replies
155
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 8 hours ago by
i.sudbery
19k • written 11 hours ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
104
views
student
epitranscriptomics
updated 11 hours ago by
ATpoint
82k • written 12 hours ago by
useriwa
• 0
0
votes
0
replies
63
views
Imputation of missing genotypes
panel
beagle
imputation
12 hours ago by
analyst
▴ 30
0
votes
3
replies
123
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 9 hours ago by
GenoMax
142k • written 12 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
59
views
Correlation Analysis
statistics
methylation
NGS
expression
13 hours ago by
Researcher
▴ 30
1
vote
2
replies
123
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
7 hours ago by
robert.flynn.21
• 0
1
vote
1
reply
92
views
Gene density plot
density
gene
updated 8 hours ago by
dthorbur
★ 1.9k • written 14 hours ago by
gubrins
▴ 290
1
vote
4
replies
143
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex
bwt
1 hour ago by
qwertyuiop26
• 0
0
votes
0
replies
78
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
1 day ago by
Scott McKay
▴ 30
0
votes
0
replies
80
views
Cellphonedb results
cpdb
visulization
cellphonedb
1 day ago by
piotto
▴ 20
0
votes
0
replies
87
views
Cox Model with interaction item interpretation
Cox
1 day ago by
Bine
▴ 60
0
votes
0
replies
79
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
1 day ago by
Javier
• 0
1
vote
6
replies
403
views
Question regarding WGCNA
WGCNA
Network-construction
updated 8 hours ago by
andres.firrincieli
3.6k • written 4 days ago by
deepak
• 0
0
votes
0
replies
87
views
vdjtools
vdjtools
1 day ago by
yueli7
▴ 250
0
votes
1
reply
137
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 12 hours ago by
andres.firrincieli
3.6k • written 1 day ago by
Antonio
• 0
0
votes
0
replies
97
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
86
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
98
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
105
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
113
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
2 days ago by
DGTool
• 0
0
votes
0
replies
121
views
Seurat V5 integration
Seurat
samples
integration
combine
2 days ago by
starswillfade
▴ 10
0
votes
1
reply
175
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
252
views
creating batch colum for batch correction
batch-correction
combat
1 day ago by
Expert
▴ 10
0
votes
1
reply
207
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
148
views
Homer motif analysis
Homer
3 days ago by
daffodil
▴ 10
0
votes
4
replies
289
views
HCL database download
database
HCL
human
updated 11 hours ago by
GenoMax
142k • written 3 days ago by
sooni
▴ 20
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
412
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
274
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
229
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
213
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
297
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
3
votes
5
replies
277
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
281
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
449 results • Page
1 of 9
Recent Votes
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?
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
Answer: TFs and Gene databases
Answer: TFs and Gene databases
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jared.andrews07
★ 16k
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▴ 100
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Recent Replies
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
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★ 2.0k
I had hoped things like [this Jupyter notebook for the rabbit data analysis](https://nbviewer.org/github/tanaylab/rabembflow/blob/master/2-…
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by
1769mkc
★ 1.2k
please provide the design matrix mean the metadata of the model fit2 which is there in the code . i guess other users can help
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by
JACKY
▴ 140
The repo does not provide any valuable information unfortunately. The Metacell algorithm they provide in the vignette is missing the metagr…
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