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116,012 results • Page
1 of 2321
Sort: Rank
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Votes
Replies
0
votes
3
replies
141
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
just now by
Nitin
• 0
0
votes
1
reply
15
views
(sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
scRNA-seq
updated just now by
Ram
43k • written 24 minutes ago by
chiditatawmbi
• 0
0
votes
0
replies
18
views
Normalization strategies for comparing mapped reads across samples in RNA-seq
normalization
rnaseq
58 minutes ago by
Picasa
▴ 640
0
votes
0
replies
21
views
How to change alternate conformation occupancy ?
Module
Bio.PDB.Atom
Bio.PDB
updated 1 hour ago by
GenoMax
140k • written 1 hour ago by
udakshi
• 0
0
votes
0
replies
23
views
Training
chip-seq
ScATAC-seq
1 hour ago by
Manhezz
• 0
1
vote
2
replies
45
views
Issue with making local BLAST database
database
mitochodrial
diatoms
blast
ncbi
28 minutes ago by
Begonia_pavonina
▴ 140
1
vote
1
reply
239
views
diffbind : killed dba.count(DBsample, bParallel=FALSE)
diffbind
r
atacseq
2 hours ago by
Pierre Lindenbaum
160k
0
votes
1
reply
44
views
ONT direct RNA sequencing
gz
DRS
ONT
gunzip
gzip
updated 2 hours ago by
dthorbur
★ 1.7k • written 2 hours ago by
Karina
• 0
0
votes
1
reply
43
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 2 hours ago by
ATpoint
81k • written 2 hours ago by
gdfsnkfns
• 0
1
vote
8
replies
125
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
1 hour ago by
Lila M
★ 1.2k
793
votes
167
replies
139k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 9 weeks ago by
Biostar
2.6k • written 7.3 years ago by
Istvan Albert
100k
1
vote
1
reply
55
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
updated 3 hours ago by
Ram
43k • written 3 hours ago by
Pumla
• 0
0
votes
1
reply
61
views
Merging featureCounts output for different species
featureCount
RNAseq
updated 4 hours ago by
andrebolerbarros
• 0 • written 4 hours ago by
Christian
• 0
2
votes
2
replies
73
views
Interproscan taking so much time
slurm
interproscan
transcriptomics
updated 4 hours ago by
dthorbur
★ 1.7k • written 4 hours ago by
Mohamed Abderrahmane
▴ 10
0
votes
0
replies
38
views
Combine rename and rmdup in SeqKit to remove duplicate sequences and append N in header? Sort by occurence?
seqkit
fasta
4 hours ago by
Broccoli
• 0
0
votes
0
replies
41
views
Is there a good tool/reference for PBP and porin analysis
PBP
porin
4 hours ago by
blur
▴ 280
0
votes
0
replies
48
views
meta-analysis on RNA seq AND microarray results
microarray
RNA
5 hours ago by
liuyibin2005
• 0
49
votes
30
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 2 hours ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
0
votes
0
replies
38
views
SPOTlight deconvolution logFC, logFC cohen or mean.AUC
spatial-transcriptomics
SPOTlight
logFC
deconvolution
updated just now by
Ram
43k • written 6 hours ago by
M'zelle
• 0
0
votes
5
replies
162
views
calculate mismatch rate from VCF file
mismatch-rate
VCF
updated just now by
Ram
43k • written 11 hours ago by
Dora
▴ 10
2
votes
3
replies
258
views
Hybrid assembly Pacbio- Nanopore
long-reads
hybric
assembly
genome
short-reads
updated 6 hours ago by
colindaven
6.3k • written 2 days ago by
Lissa Cruz Saavedra
• 0
0
votes
0
replies
58
views
In scRNA, How should I set QC standards?
scRNA
QC
8 hours ago by
mnx0723
• 0
0
votes
0
replies
49
views
Annotation of Complex genomes using NCBI Genome Workbench
Genome-Workbench
MAKER
updated just now by
Ram
43k • written 10 hours ago by
SAsciences
• 0
0
votes
2
replies
223
views
Error occurs when migrate-n software performs "make mpis"
migrate-n
10 hours ago by
lingxue
• 0
0
votes
0
replies
59
views
How to check if a few pathways have relationship?
MSigdb
REACTOME
KEGG
12 hours ago by
Chris
▴ 260
2
votes
10
replies
695
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated just now by
Ram
43k • written 5 weeks ago by
Sky
▴ 10
3
votes
2
replies
265
views
FDR and Bonferroni
FDR
Bonferroni
updated 12 hours ago by
joe
▴ 470 • written 2 days ago by
song
• 0
0
votes
1
reply
469
views
Which fasta files are assembled transcripts IDBA_tran assembler ?
RNA-Seq
Assembly
updated 15 hours ago by
weidonglu
• 0 • written 3.8 years ago by
sunnykevin97
▴ 980
0
votes
0
replies
74
views
doing some ontology enrichment analysis
GO
15 hours ago by
aleksk779
• 0
2
votes
1
reply
166
views
Choosing an FC Threshold
statistics
rna-seq
updated 14 hours ago by
Gordon Smyth
★ 6.9k • written 1 day ago by
Netanel
• 0
0
votes
1
reply
107
views
Converting AutoDock-Vina PDBQTs to PDB files
Docking
AutoDock
Vina
PDBQT
PDB
updated 17 hours ago by
Mensur Dlakic
★ 26k • written 1 day ago by
Ricard
• 0
0
votes
2
replies
145
views
novel and know mir156 and mir172
a
updated 14 hours ago by
gayachit
▴ 200 • written 18 hours ago by
Fadmo
• 0
0
votes
1
reply
93
views
Update R in Posit Workbench
R
Posit
updated 19 hours ago by
Ram
43k • written 19 hours ago by
Nitin
• 0
2
votes
8
replies
233
views
Piping samtools to R
R
NGS
bash
samtools
19 hours ago by
joe
▴ 470
8
votes
6
replies
384
views
Pangenome of plant
pangenome
plant
updated 21 hours ago by
talbots
• 0 • written 1 day ago by
analyst
▴ 10
1
vote
2
replies
173
views
vg call is time consuming
vg
20 hours ago by
Maxine
▴ 40
4
votes
14
replies
4.5k
views
8 follow
Installation: Tax4Fun2 package are not found and github repository is not maintained anymore
Tax4Fun2
updated 20 hours ago by
Ram
43k • written 21 months ago by
Elsa
▴ 20
0
votes
8
replies
402
views
STAR aligner options
STAR
4 hours ago by
theophile
• 0
2
votes
3
replies
503
views
Website or tool to obtain a list of genes that participate in a specific process?
genomics
updated 22 hours ago by
NancyTLi
• 0 • written 3 months ago by
Hamtaro
▴ 50
0
votes
2
replies
290
views
How to obtain Node/ Edge information from a Reactome Pathway
R
API
pathways
reactome
databases
updated 21 hours ago by
GenoMax
140k • written 4 weeks ago by
K.patel5
▴ 140
0
votes
2
replies
154
views
Why counting by diffbind and featurecounts differ?
featurecounts
diffbind
16 hours ago by
Ankit
▴ 500
0
votes
1
reply
101
views
Wanting to make a Venn diagram of ATACseq peak files, unsure of where to start
ATAC-seq
updated 21 hours ago by
Yogi
▴ 70 • written 22 hours ago by
Ronin
• 0
0
votes
0
replies
78
views
Association Module to traits
module-trait-relationships
WGCNA
GENIE3
DOMINO
updated 21 hours ago by
Ram
43k • written 23 hours ago by
r.shiasi3897
▴ 10
0
votes
0
replies
78
views
Number of pathway result from GSVA
GSVA
23 hours ago by
Chris
▴ 260
0
votes
1
reply
116
views
How can I remove duplicate SNP?
plink
updated 23 hours ago by
iraun
6.2k • written 23 hours ago by
Zhennan
• 0
0
votes
1
reply
128
views
SNP VCF files from hybrid populations and parental populations generated by GBS in public databases
contaminations
verification
parental
check
updated 21 hours ago by
Ram
43k • written 1 day ago by
Hajar
• 0
0
votes
0
replies
75
views
Creating a custom ontology for peptides
ontology
peptide
1 day ago by
Mathew
• 0
0
votes
3
replies
207
views
convert cds to seurat object
R
monocle3
seurat
updated 3 hours ago by
edoardofilippi1998
• 0 • written 1 day ago by
sooni
▴ 20
0
votes
0
replies
76
views
GSEA number dimension of expression dataset
GSEA
1 day ago by
edoardofilippi1998
• 0
0
votes
2
replies
211
views
Limma compare between 3 conditions vs 2 conditions
Limma
23 hours ago by
Chris
▴ 260
116,012 results • Page
1 of 2321
Recent Votes
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
Crispr-cas9 screen analysis mageck
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Devon Ryan
104k
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to
amitpande74
▴ 20
Scholar
to
Pierre Lindenbaum
160k
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beacamara
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blur
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Recent Replies
Answer: 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' combin…
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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