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1,000 results • Page
5 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
198
views
SeuratDisk: including "counts" dataset in conversion to AnnData
Seurat
SeuratDisk
AnnData
updated 19 days ago by
Ram
43k • written 19 days ago by
roussine
▴ 10
0
votes
0
replies
188
views
I am getting more annotation hits from HOMER than I have actual peaks. Is that normal?
ATAC-seq
HOMER
19 days ago by
Ronin
• 0
4
votes
13
replies
915
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 15 days ago by
BioinfGuru
★ 1.7k • written 20 days ago by
matteo.levorato
• 0
2
votes
1
reply
261
views
VEP annotation --per_gene allele choice
VEP
updated 19 days ago by
Ram
43k • written 19 days ago by
atariw
▴ 10
0
votes
2
replies
296
views
Are GeneExpression Subtype annotations removed from TCGA-GBM?
tcga-gbm
subtyping
tcga
updated 19 days ago by
Zhenyu Zhang
★ 1.2k • written 19 days ago by
Apollonia
• 0
1
vote
1
reply
254
views
RNA seq normalization and gene gene correlation
rna-seq
pearson-correlation
vst
updated 19 days ago by
Ram
43k • written 19 days ago by
Fish
• 0
0
votes
0
replies
193
views
Snakemake fails to find conda in PBS
snakemake
19 days ago by
yixinzeng
• 0
0
votes
0
replies
193
views
KaryoPlot: Gene coverage over centromeric regions
Gene
coverage
Centromere
Bedtools
19 days ago by
Mary
• 0
0
votes
0
replies
186
views
Protein stability analysis
mutation
analysis
19 days ago by
marco.barr
▴ 80
1
vote
4
replies
407
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics
htseq-count
RNA-Seq
NGS
hisat2
updated 18 days ago by
BioinfGuru
★ 1.7k • written 19 days ago by
Morteza
• 0
3
votes
1
reply
274
views
how to change the gene header names in a fasta file?
fasta
bioawk
awk
seqkit
updated 20 days ago by
Ram
43k • written 20 days ago by
rj.rezwan
• 0
0
votes
0
replies
176
views
Multiple Spike-Ins
MeRIP
Spike-In
20 days ago by
Adam
▴ 30
0
votes
0
replies
164
views
Tools for Sequence Consensus
Consensus-Sequence
bacteria
updated 20 days ago by
Ram
43k • written 20 days ago by
Reno
• 0
2
votes
2
replies
286
views
DepMap: siRNA and CRSIPR discrepancy
DepMap
updated 20 days ago by
ATpoint
82k • written 20 days ago by
Shicheng Guo
★ 9.4k
1
vote
0
replies
165
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
20 days ago by
eesiribloom
▴ 80
0
votes
3
replies
335
views
10x GEX and ADT data analysis in Seurat
Seurat
scRNA-seq
ADT
Cite-seq
GEX
updated 18 days ago by
ATpoint
82k • written 20 days ago by
gdfsnkfns
• 0
0
votes
4
replies
335
views
Questions about transfering wgs file to reference genome file
fasta
cram
genome
20 days ago by
me
• 0
0
votes
2
replies
278
views
WGCNA
PCA
WGCNA
EIGENGENE
20 days ago by
rajasekargutha
▴ 60
0
votes
3
replies
284
views
BLASTP web- <20aa peptides- interpreting results/ minimum E value?
blast
peptide
blastp
alignment
updated 20 days ago by
GenoMax
141k • written 20 days ago by
neish
• 0
1
vote
0
replies
162
views
DESeq2 comparing timepoints within treatment and account for background control change
RNAseq
DEG
DESeq2
updated 20 days ago by
Ram
43k • written 20 days ago by
ian.will
▴ 30
0
votes
0
replies
111
views
Surrogate variable analysis for paired RNA seq experiment
sva
rnaseq
ruvseq
20 days ago by
nhaus
▴ 310
1
vote
3
replies
296
views
True variants selection
vcf
bcftools
updated 19 days ago by
dthorbur
★ 1.9k • written 20 days ago by
maevalefeuvre
• 0
0
votes
1
reply
176
views
How to reveal real AF of variant if duplicates can't be removed (such as in amplicon-seq)
allele-frequency
amplicon-seq
updated 20 days ago by
Ram
43k • written 20 days ago by
CY
▴ 750
0
votes
0
replies
115
views
Creating a BSgenome data package from a NCBI assembly - Virus
Virus
BSgenomeForge
BSgenome
R
20 days ago by
JirMan
▴ 20
1
vote
1
reply
181
views
Failed to download data from EBI with ascp
EBI
aspera
updated 20 days ago by
GenoMax
141k • written 20 days ago by
biock
▴ 60
0
votes
0
replies
405
views
BETA whether on the same scale when performing rank-based inverse normal transformation on the same type of phenotype data for two cohorts separately…
normal
inverse
transformation
20 days ago by
Isaac
• 0
0
votes
0
replies
116
views
Combining VG graphs
vg
graphs
combine
21 days ago by
AshleeThomson
▴ 80
0
votes
0
replies
120
views
Installing SALSA and HIRise scafolding software
scafolding
SALSA
genome-assembly
HIRise
updated 20 days ago by
Ram
43k • written 21 days ago by
Lissa Cruz Saavedra
• 0
0
votes
1
reply
191
views
Extract Di-nucleotide/Tri-Nucleotide substitution frequencies from MSA/VCF file
MSA
substitution
VCFstats
Evolution
VCF
updated 21 days ago by
Pierre Lindenbaum
161k • written 21 days ago by
Saran
▴ 50
0
votes
2
replies
284
views
Abundance Calculation in MetaPhlAn 3: Methodology, TPM or RPKM, and the Treatment of Unclassified Reads
MetaPhlAn
Normalization
RPKM
TPM
19 days ago by
ramin.k2013
• 0
0
votes
0
replies
166
views
Normalization in Metagenomics Sequencing By Total Number of Reads: Pre- or Post-Filtering and the Role of Unclassified Reads
Normalization
Metagenomics
updated 20 days ago by
Ram
43k • written 21 days ago by
ramin.k2013
• 0
0
votes
1
reply
184
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
updated 21 days ago by
Pierre Lindenbaum
161k • written 21 days ago by
sainavyav22
• 0
0
votes
9
replies
609
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 20 days ago by
LauferVA
4.2k • written 21 days ago by
Aki
▴ 20
0
votes
0
replies
102
views
Issue while using circle_dat function from GOplot in R
GOplot
R
21 days ago by
ckelly96
• 0
0
votes
2
replies
212
views
Can't figure out plink --sample-diff
plink
21 days ago by
curious
▴ 750
0
votes
1
reply
160
views
Geneious Prime (Consense Sequence)
Consense
Sequence
updated 21 days ago by
GenoMax
141k • written 21 days ago by
Reno
• 0
1
vote
2
replies
238
views
convert a seurat object to expressionset
Seurat
20 days ago by
Bine
▴ 60
2
votes
4
replies
415
views
Per Base Sequence Content - continuous raise of G%
fastqc
updated 21 days ago by
GenoMax
141k • written 22 days ago by
pl.terzian
• 0
0
votes
0
replies
127
views
Inferring cell identity/genotype in single cells with missing information
cell
seurat
single
score
21 days ago by
txema.heredia
▴ 110
0
votes
0
replies
108
views
cibersortx colnames
gema122
21 days ago by
gem1
• 0
0
votes
2
replies
234
views
How to detect and visualize ORFs in bacterial genome?
statistics
visualization
ORFs
genome
19 days ago by
marongiu.luigi
▴ 710
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 22 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
0
votes
0
replies
109
views
Confused about the results of a function in dada2 pipeline sample inference step
Microbiome
R
dada2
22 days ago by
Mohamed Samir
▴ 20
1
vote
4
replies
829
views
I want to calculate if the sample has whole genome duplication event or not?
sequencing
wgs
22 days ago by
Hyper_Odin
▴ 310
2
votes
4
replies
312
views
Addmetadata to seurat obj
seurat
21 days ago by
synat.keam
▴ 100
0
votes
0
replies
105
views
Methylation array analysis using dmpFinder
epic
methylation
normalization
dmp
mset
22 days ago by
Roy
▴ 10
0
votes
0
replies
197
views
Confused by the `--ld-window` flag in Vcftools. What does the number of SNPs between SNPs mean?
tabix
vcftools
22 days ago by
rijan_dhakal2055
• 0
0
votes
5
replies
411
views
Used featureCounts to generate a count matrix for sc RNA-seq and it has all 0s.
scRNA-seq
updated 21 days ago by
GenoMax
141k • written 22 days ago by
Shay
• 0
0
votes
0
replies
110
views
Databases with GoF (Gain of Function) annotations.
gof
lof
gain-of-function
22 days ago by
_quantum_girl_
▴ 10
0
votes
2
replies
259
views
Problem with downloading genome in SnpEff
SnpEff
21 days ago by
Javier
• 0
1,000 results • Page
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Comment: POSSUM not working due to incompatible pssm file
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Answer: NGS forensics: how to know if data is fabricated
Comment: Adjust pvalue in R with different approach give me all different outcome
Comment: Bacterial plasmid analysis
Comment: DESeq2 processing problems
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Comment: Odd alignment question/finding
by
liorglic
★ 1.4k
I can't come up with an explanation, but two things you can try for debugging are: 1) look at the fastp stats - do they add up and make sen…
Answer: Bacterial plasmid analysis
by
Mensur Dlakic
★ 27k
If you put all your sequences in separate files but in the same directory, this program will build a cladogram based on average nucleotide …
Comment: POSSUM not working due to incompatible pssm file
by
rianna.collins
• 0
Thank you so much. I'm new to this and didn't realise there was a code option.
Answer: Is there a way to increase the automatic label text size in Cytoscape?
by
Scooter
▴ 280
Greetings, Are you saying that you can't use the size setting in the style tab? That should certainly work, as should the label size se…
Answer: Basic stats in hierfstat
by
mdav
• 0
Hi Zoe, did you find an answer for this? I am also getting the same error.
Comment: GATK won't produce figures while analyzing covariates to generate 'recal_plots.p
by
GenoMax
141k
Your cluster may be missing libraries etc to create the PDF plots (this looks like a cluster job submission) on your cluster. Did you check…
Comment: Post-imputation plot
by
kl
▴ 10
Ok yes I think my thought was that given these errors, I could remove the mismatches and flip the alleles which seem to need flipping based…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
I think I will perhaps use their predominant PlasmidFinder type to group plasmids together and create separate core phylogenies for each as…
Comment: Bacterial plasmid analysis
by
GenoMax
141k
Can you classify the plasmids based on function (resistance genes they are carrying or some other criteria). Sizes above are indicating a w…
Comment: DESeq2 processing problems
by
ATpoint
82k
Initially posted here https://support.bioconductor.org/p/9158036/ where I suggested to put code and data and noted that GEOquery returns ar…
Answer: Post-imputation plot
by
LChart
3.9k
I agree that some need to be flipped (A/T and C/G where your panel frequency is 1 - ref panel frequency). There are other variants which yo…
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by
Adam
▴ 30
Are those 20% unaligned reads coming after hyper-editing detection?
Answer: How to find overlap of clusters in two seurat porject
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Adam
▴ 30
I think your best bet would be to use annotation mapping. You can use the features of your clusters in group 1 and apply them to group 2 to…
Answer: DESeq2 processing problems
by
Adam
▴ 30
> when I put in the dataset, I am not able to run it for DEG analysis because system asks me to remove the first column which is of gene na…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
Thank you so much for your quick response, I have been searching scientific papers for about a week but have failed to come up with a reaso…
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