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824 results • Page
2 of 17
Sort: Rank
Rank
Views
Votes
Replies
0
votes
2
replies
212
views
Limma compare between 3 conditions vs 2 conditions
Limma
23 hours ago by
Chris
▴ 260
0
votes
0
replies
84
views
single cell data integration approach
comparison
integration
pairwise
singlecell
1 day ago by
Jay
• 0
0
votes
3
replies
211
views
High number of detected genes per cell after doublet removal - scRNAseq data
scRNAseq
duoblet
1 day ago by
sarahmanderni
▴ 100
1
vote
1
reply
200
views
DESeq2 and normalization
RNA-seq
normalization
DESeq2
updated 1 day ago by
GenoMax
140k • written 1 day ago by
JH
• 0
0
votes
2
replies
149
views
Error with goodSamplesGenes()
R
WGCNA
21 hours ago by
bioinfo_enthusiast
• 0
0
votes
0
replies
90
views
Variant Enrichment Analysis
Analysis
Enrichment
VEP
Variant
1 day ago by
Mojtaba
• 0
0
votes
7
replies
309
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 15 hours ago by
GenoMax
140k • written 1 day ago by
Patadu94
• 0
0
votes
1
reply
141
views
dbsnp flanks information
dbsnp
updated 1 day ago by
Pierre Lindenbaum
160k • written 1 day ago by
sskimvd
• 0
0
votes
1
reply
136
views
Cell communacations analysis. I only have the proteome of one type of cell
How
to
updated 1 day ago by
ATpoint
81k • written 1 day ago by
David Arturo
• 0
0
votes
0
replies
100
views
bulk RNA-seq: how to remove batch effect between multiple batches and labels?
combat
batch
1 day ago by
kiraqueen
• 0
2
votes
2
replies
205
views
A pipeline for prediction and annotation of obelisks
rna-seq
updated 23 hours ago by
Pierre Lindenbaum
160k • written 1 day ago by
fred.s.kremer
▴ 110
6
votes
12
replies
5.5k
views
6 follow
Getting sample information from GEO
GEO
NCBI
updated 1 day ago by
Tania
• 0 • written 6.8 years ago by
Tom_L
▴ 350
0
votes
0
replies
99
views
Convert VCF file and add covariate information
VCF
PED
PLINK
1 day ago by
asmariyaz23
▴ 10
0
votes
0
replies
99
views
Merging Hi-C datasets originating from experiments using different enzymes
enzymes
Hi-C
updated 1 day ago by
Ram
43k • written 1 day ago by
hamarillo
▴ 70
0
votes
2
replies
214
views
Using the Ontology Lookup Service (OLS) API
API
OLS
1 day ago by
longoka
▴ 40
7
votes
2
replies
198
views
Create a new reference genome with denovo assembly and standard reference with long read data?
PacBio
updated 1 day ago by
gconcepcion
▴ 410 • written 1 day ago by
eorr
▴ 30
2
votes
3
replies
237
views
Extracting information from my VCF file
VCF
updated 1 day ago by
bioruffo
▴ 40 • written 1 day ago by
realtreeecat
• 0
0
votes
4
replies
235
views
Coverage observed in introns in the Knockdown genes but not in knockout genes
RNA-seq
STAR
IGV
3 hours ago by
rohitsatyam102
▴ 840
0
votes
2
replies
270
views
JASPAR2024_getMatrixSet error
getMatrixSet
JASPAR2024
updated 1 day ago by
Ram
43k • written 5 weeks ago by
maplewj
▴ 10
2
votes
3
replies
450
views
Should I use Dfam or a custom repetitve elements library (from PlantRep) as a repeat database; using RepeatMasker in a Linux machine?
genome
sequence
repeatmasker
blast
updated 1 day ago by
b.contreras.moreira
▴ 70 • written 2 days ago by
Vijith
▴ 30
0
votes
0
replies
89
views
How to access an image (slice) of interest in spatial analysis
spatial-transcriptomics
Seurat
Visium
updated 1 day ago by
Ram
43k • written 1 day ago by
piotto
▴ 20
0
votes
2
replies
184
views
Fpkm and log2fold change and pcr validation
fpkm
updated 2 days ago by
bioruffo
▴ 40 • written 2 days ago by
mounavisirekolam
• 0
2
votes
2
replies
200
views
Location of NCBI ftp site changed?
ftp
ncbi
2 days ago by
sampsa.hyvamaki
• 0
0
votes
1
reply
162
views
MACS3 or SEACR
MACS3
SEACR
updated 2 days ago by
jared.andrews07
★ 16k • written 2 days ago by
daffodil
▴ 10
0
votes
0
replies
115
views
Visium dataset distance between spots calculations
SpatialSeq
Visium
updated 2 days ago by
GenoMax
140k • written 2 days ago by
houssi301
• 0
0
votes
0
replies
95
views
Best codeml model for estimating omega, M0 ?
codeml
ete3
evol
2 days ago by
Adrian Pelin
★ 2.6k
1
vote
1
reply
152
views
Pool-Seq same as normal variant calling?
Pool-Seq
Variant-Calling
updated 1 day ago by
dthorbur
★ 1.7k • written 2 days ago by
andrebolerbarros
• 0
0
votes
1
reply
145
views
Karytotype color annotations
karyotype
annotations
chromosome
color
updated 2 days ago by
Pierre Lindenbaum
160k • written 2 days ago by
Mary
• 0
0
votes
1
reply
221
views
What alternative method would recommend for conducting gene ontology analysis?
WEGO
gene-ontology
updated 2 days ago by
dthorbur
★ 1.7k • written 3 days ago by
mathavanbioinfo
▴ 80
1
vote
11
replies
428
views
Nanopore data filtering using fastp
fastp
nanopore
59 minutes ago by
emilydolivo97
• 0
1
vote
2
replies
219
views
Is it possible to see so little adipocyte in white adipose tissue?
scRNA-seq
1 day ago by
kayah
• 0
2
votes
2
replies
224
views
singlecell annotation
scRNA-seq
annotation
1 day ago by
kayah
• 0
3
votes
12
replies
631
views
Facing problem with extracting phenotypic data from GEO
WGCNA
GEO
1 day ago by
bioinfo_enthusiast
• 0
0
votes
1
reply
145
views
Autodock tools error - The requested operation requires lifting
Autodock
MGLTools
updated 2 days ago by
zx8754
11k • written 2 days ago by
DOMENICA ALEXANDRA
• 0
0
votes
0
replies
105
views
t2t Reference gtf file
t2t
2 days ago by
Emre
• 0
1
vote
2
replies
229
views
BWA MEM Alignment mapped small part of the reads!!
bwa
mem
updated 1 day ago by
bioruffo
▴ 40 • written 2 days ago by
Bunit
• 0
1
vote
0
replies
96
views
Job:
Job Opening - Fred Hutch - Director of Training & Community
fred-hutchinson
updated 1 day ago by
Ram
43k • written 2 days ago by
Fred Hutch (Recruiting)
▴ 20
0
votes
0
replies
106
views
Correlation analysis in single-cell sequencing data
scRNA-seq
correlation
scATAC-seq
2 days ago by
Yingying
• 0
0
votes
0
replies
104
views
MIENTURNET - miRNA enrichment analysis
miRNA-enrichment
mRNA
RNA
updated 2 days ago by
Ram
43k • written 2 days ago by
PBC
▴ 10
0
votes
4
replies
261
views
Parsing fasta file by coordinates
linux
fasta
updated 3 hours ago by
Joe
21k • written 2 days ago by
sorrymouse
▴ 120
0
votes
2
replies
216
views
comparing VCF files
long-reads
VCF
variants
ONT
nanopore
1 day ago by
eesiribloom
▴ 50
0
votes
2
replies
203
views
Using velocyto on 3'UTR 10x single-cell RNA-Seq data
single-cell
single-end
10x
velocyto
2 days ago by
Sergio
• 0
0
votes
0
replies
125
views
Job:
Post-doctoral positions in computational biomedicine
data-science
biomedicine
machine-learning
updated 2 days ago by
Ram
43k • written 2 days ago by
pandey.gaurav
▴ 200
6
votes
13
replies
469
views
Allocating right resources to HPC using LSF scheduler
BWA
GATK
hpc
lsf
bsub
2 days ago by
Maverick
▴ 10
10
votes
6
replies
4.0k
views
Tutorial:
CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation
corlevelplot
updated 1 day ago by
Ram
43k • written 6.1 years ago by
Kevin Blighe
87k
0
votes
5
replies
453
views
How to download RNAseq data of only male KIRC patients?
TCGAbiolinks
2 days ago by
bioinfo_enthusiast
• 0
0
votes
0
replies
87
views
Multifactor Analysis in DiffBind
DiffBind
ChIPseq
ChIP-seq
2 days ago by
erbrocato
• 0
0
votes
1
reply
127
views
Can I have multiple active GDC download tokens?
TCGA
updated 2 days ago by
GenoMax
140k • written 2 days ago by
mrk
• 0
0
votes
0
replies
103
views
How to calculate weighted transcript length for each gene?
salmon
tximport
rna-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
barrypraveen
▴ 130
1
vote
2
replies
222
views
Deseq generating warning "the model matrix is not full rank"
deseq
updated 1 day ago by
bioruffo
▴ 40 • written 2 days ago by
MAPK2
▴ 40
824 results • Page
2 of 17
Recent Votes
How can two contradicted gene sets be enriched in a cancer sample in GSEA analysis?
Comment: Only one read per run - Trying to use CellRangerv7
Comment: Interproscan taking so much time
Answer: Interproscan taking so much time
Comment: Volcano Plot Output Inquiry: Graphs Facing Down
A: Crispr-cas9 screen analysis mageck
A: Crispr-cas9 screen analysis mageck
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Recent Awards •
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Commentator
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Devon Ryan
104k
Popular Question
to
amitpande74
▴ 20
Scholar
to
Pierre Lindenbaum
160k
Popular Question
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beacamara
• 0
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blur
▴ 280
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ATpoint
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Recent Replies
Comment: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
Nitin
• 0
I did ran the "JoinLayers()" even then it is not working, here is the output before and after DefaultAssay(combined1) <- 'RNA' c…
Comment: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
Nitin
• 0
I tried that too. It did not work.
Comment: (sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
by
GenoMax
140k
Try SRA-explorer with search terms you want. Guide here: https://www.biostars.org/p/366721/ Check these portals: https://singlecell.broad…
Comment: Issue with making local BLAST database
by
Begonia_pavonina
▴ 140
Thank you @genomax, if I have well understood the `retmax` parameter and 10000 entries limitation are linked to the R package, and not to t…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
thank you , this is my code : import sys import os import subprocess class FastpFiltering: def __init__(self, input_folder, fastp_ou…
Comment: Nanopore data filtering using fastp
by
GenoMax
140k
You can also use `reformat.sh` from [**BBMap suite**][1]. Look at sampling options. [1]: https://sourceforge.net/projects/bbmap/
Comment: calculate mismatch rate from VCF file
by
Pierre Lindenbaum
160k
> I was using it but the output file was too big pipe the output
Comment: Nanopore data filtering using fastp
by
dthorbur
★ 1.7k
Share code and an example please.
Comment: calculate mismatch rate from VCF file
by
Dora
▴ 10
I was using it but the output file was too big, so that I thought the vcf file was more efficient. But now I know that I can stop working o…
Comment: Interproscan taking so much time
by
Mohamed Abderrahmane
▴ 10
Thank you for your reply. I have just executed the computation with parallelization as you mentioned, and I will observe the differences. H…
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Of course ... But as 'expected' the range `range=chr8:127794533-128101253` in the output sequence file belongs to: LF385466, LF385467, MA62…
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Can you select the output format as sequence instead of BED?
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Could you please elaborate how to retrieve the sequences directly from the table browser? Thanks!
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
If coordinates in your BED file refer to chromosomal locations then you need to use the whole genome file and get those sections by the met…
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
by
Istvan Albert
100k
maybe it would work better to ask the OP to post their question as a new one and delete this answer after, if you delete the post they ca…
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