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116,001 results • Page
1 of 2321
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0
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0
replies
8
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meta-analysis on RNA seq AND microarray results
microarray
RNA
32 minutes ago by
liuyibin2005
• 0
49
votes
29
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 8 minutes ago by
ATpoint
81k • written 8.1 years ago by
Ram
43k
0
votes
0
replies
7
views
SPOTlight deconvolution logFC, logFC cohen or mean.AUC
spatial
SPOTlight
transcriptomic
logFC
deconvolution
1 hour ago by
M'zelle
• 0
0
votes
1
reply
58
views
calculate mismatch rate from VCF file
rate
VCF
mismatch
updated 1 hour ago by
Pierre Lindenbaum
160k • written 6 hours ago by
Dora
▴ 10
0
votes
0
replies
11
views
Downloading a list of all refseq assembly ids, including supressed assembliey
refseq
ncbi
assembly
1 hour ago by
Bertalan_Takacs
▴ 90
1
vote
3
replies
230
views
Hybrid assembly Pacbio- Nanopore
long-reads
hybric
assembly
genome
short-reads
updated 1 hour ago by
colindaven
6.2k • written 2 days ago by
Lissa Cruz Saavedra
• 0
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
0
votes
1
reply
84
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
updated 3 hours ago by
kayah
• 0 • written 5 hours ago by
Nitin
• 0
0
votes
0
replies
30
views
In scRNA, How should I set QC standards?
scRNA
QC
3 hours ago by
mnx0723
• 0
0
votes
0
replies
30
views
Annotation of Complex genomes using NCBI Genome Workbench
annotation
Genome
MAKER
Workbench
5 hours ago by
SAsciences
• 0
0
votes
2
replies
208
views
Error occurs when migrate-n software performs "make mpis"
migrate-n
5 hours ago by
lingxue
• 0
0
votes
0
replies
42
views
How to check if a few pathways have relationship?
MSigdb
REACTOME
KEGG
7 hours ago by
Chris
▴ 260
1
vote
10
replies
676
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 6 hours ago by
GenoMax
140k • written 5 weeks ago by
Sky
▴ 10
3
votes
2
replies
245
views
FDR and Bonferroni
FDR
Bonferroni
updated 7 hours ago by
joe
▴ 470 • written 2 days ago by
song
• 0
0
votes
1
reply
456
views
Which fasta files are assembled transcripts IDBA_tran assembler ?
RNA-Seq
Assembly
updated 10 hours ago by
weidonglu
• 0 • written 3.8 years ago by
sunnykevin97
▴ 980
0
votes
0
replies
55
views
doing some ontology enrichment analysis
GO
10 hours ago by
aleksk779
• 0
2
votes
1
reply
145
views
Choosing an FC Threshold
statistics
rna-seq
updated 9 hours ago by
Gordon Smyth
★ 6.9k • written 1 day ago by
Netanel
• 0
0
votes
1
reply
88
views
Converting AutoDock-Vina PDBQTs to PDB files
Docking
AutoDock
Vina
PDBQT
PDB
updated 12 hours ago by
Mensur Dlakic
★ 26k • written 19 hours ago by
Ricard
• 0
0
votes
2
replies
119
views
novel and know mir156 and mir172
a
updated 9 hours ago by
gayachit
▴ 200 • written 13 hours ago by
Fadmo
• 0
0
votes
1
reply
82
views
Update R in Posit Workbench
R
Posit
updated 13 hours ago by
Ram
43k • written 14 hours ago by
Nitin
• 0
2
votes
8
replies
217
views
Piping samtools to R
R
NGS
bash
samtools
14 hours ago by
joe
▴ 470
8
votes
6
replies
367
views
Pangenome of plant
pangenome
plant
updated 15 hours ago by
talbots
• 0 • written 1 day ago by
analyst
▴ 10
1
vote
2
replies
163
views
vg call is time consuming
vg
15 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 15 hours ago by
Ram
43k • written 21 months ago by
Elsa
▴ 20
0
votes
6
replies
329
views
STAR aligner options
STAR
32 minutes ago by
theophile
• 0
2
votes
3
replies
496
views
Website or tool to obtain a list of genes that participate in a specific process?
genomics
updated 17 hours ago by
NancyTLi
• 0 • written 3 months ago by
Hamtaro
▴ 50
0
votes
2
replies
282
views
How to obtain Node/ Edge information from a Reactome Pathway
R
API
pathways
reactome
databases
updated 16 hours ago by
GenoMax
140k • written 29 days ago by
K.patel5
▴ 140
0
votes
2
replies
137
views
Why counting by diffbind and featurecounts differ?
featurecounts
diffbind
11 hours ago by
Ankit
▴ 500
0
votes
1
reply
89
views
Wanting to make a Venn diagram of ATACseq peak files, unsure of where to start
ATAC-seq
updated 16 hours ago by
Yogi
▴ 70 • written 17 hours ago by
Ronin
• 0
0
votes
0
replies
67
views
Association Module to traits
module-trait-relationships
WGCNA
GENIE3
DOMINO
updated 16 hours ago by
Ram
43k • written 17 hours ago by
r.shiasi3897
▴ 10
0
votes
0
replies
71
views
Number of pathway result from GSVA
GSVA
18 hours ago by
Chris
▴ 260
0
votes
1
reply
106
views
How can I remove duplicate SNP?
plink
updated 18 hours ago by
iraun
6.2k • written 18 hours ago by
Zhennan
• 0
0
votes
1
reply
118
views
SNP VCF files from hybrid populations and parental populations generated by GBS in public databases
contaminations
verification
parental
check
updated 16 hours ago by
Ram
43k • written 19 hours ago by
Hajar
• 0
0
votes
0
replies
68
views
Creating a custom ontology for peptides
ontology
peptide
19 hours ago by
Mathew
• 0
0
votes
2
replies
171
views
convert cds to seurat object
R
monocle3
seurat
7 hours ago by
sooni
▴ 20
0
votes
0
replies
68
views
GSEA number dimension of expression dataset
GSEA
19 hours ago by
edoardofilippi1998
• 0
0
votes
2
replies
203
views
Limma compare between 3 conditions vs 2 conditions
Limma
18 hours ago by
Chris
▴ 260
0
votes
0
replies
77
views
single cell data integration approach
comparison
integration
pairwise
singlecell
20 hours ago by
Jay
• 0
0
votes
3
replies
201
views
High number of detected genes per cell after doublet removal - scRNAseq data
scRNAseq
duoblet
18 hours ago by
sarahmanderni
▴ 100
1
vote
1
reply
193
views
DESeq2 and normalization
RNA-seq
normalization
DESeq2
updated 21 hours ago by
GenoMax
140k • written 1 day ago by
JH
• 0
0
votes
2
replies
141
views
Error with goodSamplesGenes()
R
WGCNA
16 hours ago by
bioinfo_enthusiast
• 0
0
votes
0
replies
85
views
Variant Enrichment Analysis
Analysis
Enrichment
VEP
Variant
22 hours ago by
Mojtaba
• 0
0
votes
7
replies
293
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 10 hours ago by
GenoMax
140k • written 23 hours ago by
Patadu94
• 0
0
votes
1
reply
134
views
dbsnp flanks information
dbsnp
updated 1 day ago by
Pierre Lindenbaum
160k • written 1 day ago by
sskimvd
• 0
0
votes
1
reply
133
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
95
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
199
views
A pipeline for prediction and annotation of obelisks
rna-seq
updated 18 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
97
views
Convert VCF file and add covariate information
VCF
PED
PLINK
1 day ago by
asmariyaz23
▴ 10
0
votes
0
replies
97
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
116,001 results • Page
1 of 2321
Recent Votes
Answer: TSS of protein coding genes
TSS of protein coding genes
Answer: vcf not indexing
Comment: Hybrid assembly Pacbio- Nanopore
Answer: vg call is time consuming
Answer: FDR and Bonferroni
Answer: FDR and Bonferroni
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81k
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Recent Replies
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
by
ATpoint
81k
I will delete this as it - obviously - does not belong into this thread.
Comment: STAR aligner options
by
theophile
• 0
I searched the different options to increase the sensitivity. As per `--seedSearchStartLmax`, I found several answer from Alexander Dobin o…
Comment: STAR aligner options
by
theophile
• 0
Sorry, I was a bit confused by the layout, thanks for editing and clarifying!
Answer: calculate mismatch rate from VCF file
by
Pierre Lindenbaum
160k
> I want to calculate the mismatch rate on base-level, samtools stats in.bam | grep "error rate" | cut -f 2,3 error rate: 2.0…
Answer: Hybrid assembly Pacbio- Nanopore
by
colindaven
6.2k
If you have sufficient coverage of Pacbio HiFi reads - I think 30- 50X - then just use the Hifiasm https://github.com/chhylp123/hifiasm. It…
Answer: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
kayah
• 0
you should run JoinLayers() before FindAllMarkers()!!
Answer: Error occurs when migrate-n software performs "make mpis"
by
lingxue
• 0
Thank you very much. I will try to install it again according to your suggestion.
Comment: Only one read per run - Trying to use CellRangerv7
by
GenoMax
140k
https://www.ncbi.nlm.nih.gov/sra/?term=SRR16053948 Metadata indicates that this is: > Single-cell combinatorial-indexing RNA-sequencing (…
Comment: Paired layout, but one fastq file
by
GenoMax
140k
There is a BAM file available here: https://sra-pub-src-2.s3.amazonaws.com/SRR14667226/CTRL_possorted_genome_bam.bam.1 Please get that wit…
Comment: Only one read per run - Trying to use CellRangerv7
by
dsull
★ 5.6k
1. This is a comment, not an answer. Please don't post it as an answer. :) 2. This is sci-rna-seq, not 10x rna-seq. CellRanger would not …
Comment: Only one read per run - Trying to use CellRangerv7
by
Sky
▴ 10
Sorry for the delayed reply. I have included my code and the output from downloading the four files. Each dataset only resulted in one fast…
Answer: FDR and Bonferroni
by
joe
▴ 470
> Any idea why this is happening? For example, I got 1064 significant > probes from raw p-values, but only 18 from Bonferroni correction, a…
Comment: Paired layout, but one fastq file
by
Sky
▴ 10
I am also having a similar issue where there is only one fastq file but no bam file available so from my understanding I can't use bamtofas…
Comment: convert cds to seurat object
by
sooni
▴ 20
Yes, I tried with `as.Seurat`. But there is an error follwing: Error: `No data in provided assay - logcounts`. How can I solve this problem?
Comment: novel and know mir156 and mir172
by
gayachit
▴ 200
Do you have RNAseq or small RNAseq data?
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