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1,000 results • Page
1 of 20
Sort: Rank
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Views
Votes
Replies
0
votes
0
replies
8
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gene_symbol
gpl
12 minutes ago by
mja
• 0
0
votes
0
replies
14
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
10 minutes ago by
Nitin
• 0
0
votes
0
replies
14
views
absolute path for symbolic links in Snakefile
Snakemake
updated 13 minutes ago by
Ram
43k • written 32 minutes ago by
yifangt86
▴ 60
0
votes
0
replies
17
views
Chemical structure validation
structure
cap
validation
metabolite
55 minutes ago by
Rodolfo Adrián
• 0
0
votes
1
reply
32
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 47 minutes ago by
GenoMax
141k • written 1 hour ago by
bioyas
▴ 10
0
votes
0
replies
39
views
Copy number variation plot
Copy-number-variation
genomics
updated 2 hours ago by
Ram
43k • written 2 hours ago by
Emmi
• 0
0
votes
0
replies
36
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
2 hours ago by
DanielEB_fisk
▴ 20
0
votes
1
reply
111
views
Could you please assist in identifying this cluster?
single-cell
updated 2 hours ago by
Ram
43k • written 3 hours ago by
Kazo
• 0
0
votes
0
replies
60
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 2 hours ago by
Ram
43k • written 5 hours ago by
Dinmukhamed
• 0
0
votes
0
replies
64
views
miRDeep2: How to get the read counts
mirdeep2
8 hours ago by
Atul K.
• 0
0
votes
0
replies
79
views
Lncipedia GTF file error
Proteomics
updated 2 hours ago by
Ram
43k • written 10 hours ago by
atharvakarkare14
▴ 10
3
votes
2
replies
226
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
3 hours ago by
joe
▴ 510
0
votes
2
replies
386
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
17 hours ago by
航太郎
• 0
0
votes
0
replies
98
views
create genewise sync file in popoolation
popoolation
updated 20 hours ago by
GenoMax
141k • written 22 hours ago by
N.Y.Wiyana-Hewage
• 0
0
votes
2
replies
248
views
python file for coding potential calculator
cpc2.py
14 hours ago by
Ashok
• 0
0
votes
2
replies
243
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
14 hours ago by
Ashok
• 0
0
votes
2
replies
266
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
11 hours ago by
Ashok
• 0
0
votes
0
replies
107
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 1 day ago by
Ram
43k • written 1 day ago by
samuelkalandarov2002
• 0
0
votes
2
replies
231
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
2 hours ago by
_quantum_girl_
▴ 10
0
votes
0
replies
114
views
traying to make a maf from an already annotated vcf
vcf2maf
VEP
maftools
updated 1 day ago by
Ram
43k • written 1 day ago by
Javier
• 0
0
votes
0
replies
105
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
1 day ago by
enferdeflame
• 0
0
votes
0
replies
115
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
22 hours ago by
Chris
▴ 260
0
votes
1
reply
387
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 1 day ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
0
votes
0
replies
126
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 1 day ago by
Ram
43k • written 1 day ago by
bioinfo223
▴ 10
0
votes
0
replies
136
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
1 day ago by
P.
• 0
0
votes
0
replies
136
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
1 day ago by
ekirsch
• 0
1
vote
1
reply
287
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
1 hour ago by
renan.igor
• 0
0
votes
0
replies
138
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
1 day ago by
synat.keam
▴ 100
0
votes
1
reply
229
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 1 day ago by
GenoMax
141k • written 1 day ago by
ycts
• 0
0
votes
4
replies
487
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
11 hours ago by
Kai Xin
• 0
1
vote
1
reply
204
views
Retrieve a % coverage for each transcript
RNA-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
jammydodger123456
▴ 40
0
votes
2
replies
322
views
How can I solve this error?
metal
1 day ago by
22211020193
• 0
0
votes
0
replies
140
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 2 days ago by
GenoMax
141k • written 2 days ago by
srimmer
• 0
1
vote
2
replies
239
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 2 days ago by
Ram
43k • written 2 days ago by
aniigodwinn
• 0
0
votes
0
replies
275
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
2 days ago by
Ronin
• 0
2
votes
7
replies
715
views
Removing duplicates
duplicates
ONT
minimap2
updated 18 hours ago by
joe
▴ 510 • written 2 days ago by
quentinperriere
• 0
0
votes
1
reply
169
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 2 days ago by
DKA
▴ 40 • written 2 days ago by
james.melhorn
• 0
0
votes
1
reply
159
views
Freyja plot error
Freyja
updated 2 days ago by
Ram
43k • written 2 days ago by
Adyasha
• 0
0
votes
0
replies
126
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
2 days ago by
chemokine-1
▴ 10
0
votes
4
replies
435
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
1 day ago by
feather-W
• 0
0
votes
2
replies
184
views
Bedmethyl file format
bedmethyl
methylation
updated 2 days ago by
GenoMax
141k • written 2 days ago by
njornet
▴ 20
0
votes
0
replies
142
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
2 days ago by
Ali
• 0
2
votes
4
replies
274
views
SnpEff annotates coding duplication as intronic?
snpeff
2 days ago by
kirill.zaslavsky
• 0
0
votes
2
replies
213
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
2 days ago by
mropri
▴ 150
0
votes
0
replies
127
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames
RNA-Seq
WGCNA
unique
2 days ago by
shasabhi1
• 0
0
votes
0
replies
121
views
How to summarize dbCAN3 results
dbCAN
CAZy
CAZyme
dbCAN3
dbCAN2
2 days ago by
Nishat
• 0
0
votes
0
replies
132
views
what exactly is a k-mer table (remora)?
remora
basecall
3 days ago by
anne
• 0
1
vote
1
reply
156
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 3 days ago by
dsull
★ 5.8k • written 3 days ago by
niruf
• 0
0
votes
0
replies
127
views
GWAS Phenotypes
GWAS
3 days ago by
solomoncharles77
▴ 90
0
votes
2
replies
286
views
GSEA analysis in R
GSEA
R
Arabidopsis
1 day ago by
Sudip
• 0
1,000 results • Page
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Recent Votes
Answer: Duplicate marking, read names, and the SRA
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Answer: Cellranger count error: Input FASTQ file ended prematurely
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
Answer: ClusterProfiler enrichKEGG – remove organism name in plots?
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Recent Awards •
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Popular Question
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Rodolfo Adrián
• 0
Scholar
to
damian.szk
▴ 70
Popular Question
to
alphaflylizard
• 0
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GenoMax
141k
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Shicheng Guo
★ 9.4k
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DanielEB_fisk
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161k
Recent Replies
Comment: Duplicate marking, read names, and the SRA
by
Luka
• 0
>In many cases those remain recoverable using the -F option when you dump the data (cloud download not required) The -F option (or any equ…
Answer: Duplicate marking, read names, and the SRA
by
GenoMax
141k
To be specific, not every dataset in SRA loses the original identifiers. In many cases those remain recoverable using the `-F` option when …
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
To use different versions of R and bioconductor, you don't really need RStudio. One can simply create new conda environments with the requi…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★ 1.7k
Done. Thank you.
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
by
GenoMax
141k
Perhaps add the word linux/ubuntu to the title? You have noted that the instructions are for Ubuntu in text.
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
by
BioinfGuru
★ 1.7k
Thanks @Ram I'll add that to the intro. I'm the admin on my machine so I haven't found it necessary to install any other way. I'll try a fr…
Comment: Downloading the raw microarray data from GEO
by
GenoMax
141k
No GPR files with this data unless you ask the submitters for them directly. You can find the matrix of data here: https://ftp.ncbi.nlm.nih…
Comment: Cellranger count error: Input FASTQ file ended prematurely
by
GenoMax
141k
That is odd. Thanks for following-up and providing an explanation.
Answer: Cellranger count error: Input FASTQ file ended prematurely
by
bp22
▴ 70
Dear all, The reason for the error was due to the index (I1) fastq files, for example `SI-GA-A1_1_S1_L001_I1_001.fastq.gz` having a lo…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
by
Ram
43k
Your tutorial required `sudo` and thus is not doable for a majority of people. Any alternative to `sudo snap`?
Comment: Should I apply doublet detection for each pool seperately?
by
Ram
43k
Do not delete posts that have received feedback,
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues
by
_quantum_girl_
▴ 10
They aren't merging any datasets. Just for reference the paper is this: https://www.nature.com/articles/s41380-022-01674-9#MOESM1. Citing: …
Comment: RNA seq differential expression analysis
by
BioinfGuru
★ 1.7k
https://help.galaxyproject.org/
Answer: RNA seq differential expression analysis
by
Mohamed Abderrahmane
▴ 10
The tool RSEM, which performs transcript quantification for RNA-Seq data, provides FPKM.
Comment: Illumina reads preprocessing best practice for snp calling applications
by
Enrique
• 0
Hi! I'm still interested in the step that you use for the SNP calling. Did you use `trimmomatic` or another tool for trimming before mappin…
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