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1,000 results • Page
2 of 20
Sort: Rank
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Votes
Replies
0
votes
0
replies
182
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 4 days ago by
Ram
43k • written 4 days ago by
mja
• 0
0
votes
0
replies
185
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
4 days ago by
Nitin
• 0
0
votes
0
replies
183
views
absolute path for symbolic links in Snakefile
Snakemake
updated 4 days ago by
Ram
43k • written 4 days ago by
yifangt86
▴ 60
0
votes
0
replies
177
views
Chemical structure validation
structure
cap
validation
metabolite
4 days ago by
Rodolfo Adrián
• 0
0
votes
1
reply
254
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 4 days ago by
GenoMax
141k • written 4 days ago by
bioyas
▴ 10
0
votes
0
replies
199
views
Copy number variation plot
Copy-number-variation
genomics
updated 4 days ago by
Ram
43k • written 4 days ago by
Emmi
• 0
0
votes
0
replies
171
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
4 days ago by
DanielEB_fisk
▴ 20
0
votes
1
reply
275
views
Could you please assist in identifying this cluster?
single-cell
updated 4 days ago by
Ram
43k • written 4 days ago by
Kazo
• 0
0
votes
0
replies
191
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 4 days ago by
Ram
43k • written 4 days ago by
Dinmukhamed
• 0
0
votes
0
replies
189
views
miRDeep2: How to get the read counts
mirdeep2
4 days ago by
Atul K.
• 0
0
votes
0
replies
198
views
Lncipedia GTF file error
Proteomics
updated 4 days ago by
Ram
43k • written 4 days ago by
atharvakarkare14
▴ 10
3
votes
3
replies
456
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 3 days ago by
swbarnes2
14k • written 5 days ago by
joe
▴ 510
0
votes
2
replies
528
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
5 days ago by
航太郎
• 0
0
votes
0
replies
208
views
create genewise sync file in popoolation
popoolation
updated 5 days ago by
GenoMax
141k • written 5 days ago by
N.Y.Wiyana-Hewage
• 0
0
votes
2
replies
365
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
5 days ago by
Ashok
• 0
0
votes
2
replies
406
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
4 days ago by
Ashok
• 0
0
votes
0
replies
207
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 5 days ago by
Ram
43k • written 5 days ago by
samuelkalandarov2002
▴ 10
0
votes
2
replies
414
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
4 days ago by
_quantum_girl_
▴ 10
0
votes
0
replies
197
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
1 day ago by
Javier
• 0
0
votes
0
replies
172
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
5 days ago by
enferdeflame
• 0
1
vote
1
reply
405
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 3 days ago by
Gordon Smyth
★ 7.0k • written 5 days ago by
Chris
▴ 260
0
votes
1
reply
397
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 5 days ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
0
votes
0
replies
155
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 5 days ago by
Ram
43k • written 5 days ago by
bioinfo223
▴ 10
0
votes
0
replies
170
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
5 days ago by
P.
• 0
0
votes
0
replies
163
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
5 days ago by
ekirsch
• 0
1
vote
1
reply
378
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
4 days ago by
renan.igor
• 0
0
votes
0
replies
168
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
6 days ago by
synat.keam
▴ 100
0
votes
1
reply
260
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 6 days ago by
GenoMax
141k • written 6 days ago by
ycts
• 0
0
votes
4
replies
569
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
4 days ago by
Kai Xin
• 0
1
vote
1
reply
218
views
Retrieve a % coverage for each transcript
RNA-seq
updated 6 days ago by
Ram
43k • written 6 days ago by
jammydodger123456
▴ 40
0
votes
2
replies
361
views
How can I solve this error?
metal
6 days ago by
22211020193
• 0
0
votes
0
replies
161
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 6 days ago by
GenoMax
141k • written 6 days ago by
srimmer
• 0
1
vote
2
replies
266
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 6 days ago by
Ram
43k • written 6 days ago by
aniigodwinn
• 0
0
votes
0
replies
349
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
6 days ago by
Ronin
• 0
2
votes
7
replies
799
views
Removing duplicates
duplicates
ONT
minimap2
updated 5 days ago by
joe
▴ 510 • written 6 days ago by
quentinperriere
• 0
0
votes
1
reply
191
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 6 days ago by
DKA
▴ 40 • written 6 days ago by
james.melhorn
• 0
0
votes
1
reply
178
views
Freyja plot error
Freyja
updated 6 days ago by
Ram
43k • written 6 days ago by
Adyasha
• 0
0
votes
0
replies
152
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
6 days ago by
chemokine-1
▴ 10
0
votes
4
replies
487
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
5 days ago by
feather-W
• 0
0
votes
2
replies
210
views
Bedmethyl file format
bedmethyl
methylation
updated 6 days ago by
GenoMax
141k • written 6 days ago by
njornet
▴ 20
0
votes
0
replies
165
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
6 days ago by
Ali
• 0
2
votes
4
replies
304
views
SnpEff annotates coding duplication as intronic?
snpeff
6 days ago by
kirill.zaslavsky
• 0
0
votes
2
replies
236
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
6 days ago by
mropri
▴ 150
0
votes
0
replies
139
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames
RNA-Seq
WGCNA
unique
7 days ago by
shasabhi1
• 0
0
votes
0
replies
130
views
How to summarize dbCAN3 results
dbCAN
CAZy
CAZyme
dbCAN3
dbCAN2
7 days ago by
Nishat
• 0
0
votes
0
replies
152
views
what exactly is a k-mer table (remora)?
remora
basecall
7 days ago by
anne
• 0
1
vote
1
reply
170
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 7 days ago by
dsull
★ 5.8k • written 7 days ago by
niruf
• 0
0
votes
0
replies
136
views
GWAS Phenotypes
GWAS
7 days ago by
solomoncharles77
▴ 90
0
votes
2
replies
304
views
GSEA analysis in R
GSEA
R
Arabidopsis
5 days ago by
Sudip
• 0
0
votes
0
replies
119
views
Add geno header to VariantAnnotation objects
nichenet
scRNA-seq
7 days ago by
QX
• 0
1,000 results • Page
2 of 20
Recent Votes
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
Comment: TCGA2STAT Error: Firehose connection
Answer: HaplotypeCaller - only SNPs
Comment: Bwa sampe - BGI
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141k
Recent Replies
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
Istvan Albert
100k
What I mean is that no sequencing run can be calibrated to the precision where it could correctly distinguish between events with phred sco…
Comment: HaplotypeCaller - only SNPs
by
analyst
▴ 20
After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1]) [1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome. [1]: https://www.na…
Answer: Wilcox test using data slot (log normalized count values) of scRNA-seq between t
by
yxwucq
• 0
The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
Comment: How to solve this RoseTTAFold colaboratory error?
by
Mensur Dlakic
★ 27k
There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
atowns21
• 0
Hmm, okay I'm not sure what is going on, but here is what I did: 1. Downloaded a single fastq: `parallel-fastq-dump --tmpdir . --threads …
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
by
HyperEvo
• 0
Ok, thank you so much~
Comment: GTF file for Rhinolophus sinicus
by
GenoMax
141k
I was able to get the GTF file. I tried the fasta genome and it seemed to work but I did not complete the download. If you choose to ignore…
Comment: some error in building kraken2 database
by
Art1ess
• 0
I have 2 files output, no error logs... the .kreport file: 100.00 160136511 160136511 U 0 unclassified head .res…
Comment: TCGA2STAT Error: Firehose connection
by
LauferVA
4.2k
agree. from a data-centric (rather than software centric) standpoint, it shouldn't be hard to get the TCGA data you are looking for from o…
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
yep. in this case id definitely start with the grant numbers themselves as others have indicated. i did not recommend this before due to un…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
This download doesn't seem to work for me. There is a message on the website saying "Warning: contaminated. Status: RefSeq GCF_001888835.1 …
Answer: HaplotypeCaller - only SNPs
by
Pierre Lindenbaum
161k
Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
Answer: Gene set enrichment analysis differences between 2020 and 2024
by
geneontologyhelp
▴ 380
We have releases about monthly in order to keep our data accurate and reflect current understanding. In 4 years, there have been about 40 r…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
GenoMax
141k
Let us know when you find out. Would be a useful thing to know what the data looks like.
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