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1,000 results • Page
3 of 20
Sort: Rank
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Votes
Replies
0
votes
6
replies
364
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq
Nanopore
ONT
differential
expression
1 day ago by
tw_140
• 0
3
votes
2
replies
189
views
Running STAR on fastq file generated from a RNA-seq experiment
STAR
RNAseq
fastq
files
updated 3 days ago by
Darked89
4.5k • written 3 days ago by
achanda
• 0
2
votes
3
replies
293
views
DEseq2 input
DEseq2
updated 3 days ago by
ATpoint
78k • written 3 days ago by
r.shiasi3897
▴ 10
0
votes
1
reply
158
views
Combine Geoids
Geoids
NCBI
updated 3 days ago by
ATpoint
78k • written 3 days ago by
anasjamshed
▴ 120
1
vote
2
replies
239
views
Best practices for unstranded sequences in featureCounts
featurecounts
overlapping
unstranded
2 days ago by
Enrique
• 0
1
vote
1
reply
180
views
Choose between pvalue & pvalue.adj
volcanoplot
updated 3 days ago by
Istvan Albert
99k • written 3 days ago by
Guitout
• 0
0
votes
5
replies
304
views
HTseq reports missing attribute name
htseq
updated 17 hours ago by
Istvan Albert
99k • written 3 days ago by
Bjorn
• 0
3
votes
0
replies
150
views
Herald:
The Biostar Herald for Monday, November 27, 2023
herald
3 days ago by
Biostar
2.3k
9
votes
15
replies
761
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
2 days ago by
analyst
▴ 10
4
votes
2
replies
1.9k
views
Masurca. Failed to pre-correct Nanopore data, please check your data!
Nanopore
Masurca
updated 3 days ago by
colindaven
5.7k • written 2.4 years ago by
kamanovae
▴ 100
0
votes
0
replies
94
views
Differentiate sequenced and imputed variants in BGEN files
imputation
bgen
ukb
3 days ago by
user230613
▴ 350
0
votes
4
replies
261
views
Species coverage in the NCBI protein NR database ?
NR
updated 3 days ago by
Istvan Albert
99k • written 3 days ago by
HERMAN
▴ 10
0
votes
7
replies
421
views
Issues while running htseq-count
Candida-glabrata
RNA-seq
htseq-count
3 days ago by
Foad
▴ 10
0
votes
0
replies
101
views
addPatternDensity to qsea object
maxDensityPattern
medip
qsea
4 days ago by
Jaykishan
• 0
1
vote
1
reply
161
views
Harmony integration PC variance explained
scRNA
integration
harmony
updated 1 day ago by
CTLong
▴ 20 • written 4 days ago by
e.iich
• 0
0
votes
3
replies
229
views
merged rs number information
merged
dbsnp
3 days ago by
sskimvd
• 0
2
votes
1
reply
152
views
Bedtools intersection
bedtools
bed
intersect
vcf
updated 3 days ago by
Pierre Lindenbaum
158k • written 4 days ago by
rejoeraymond776
▴ 10
0
votes
2
replies
198
views
RnBeads mean difference vs M-values
Methylation
updated 3 days ago by
Basti
★ 1.9k • written 4 days ago by
a.basitkhan1990
▴ 30
1
vote
2
replies
181
views
RnBeads which p-value to use
Methylation
RnBeads
updated 4 days ago by
ATpoint
78k • written 4 days ago by
a.basitkhan1990
▴ 30
1
vote
1
reply
163
views
Beginner differential methylation analysis
Methylation
updated 3 days ago by
Basti
★ 1.9k • written 4 days ago by
a.basitkhan1990
▴ 30
4
votes
8
replies
573
views
Docker: Pass reads file form host to container
docker
3 days ago by
davidmaimoun
▴ 50
2
votes
1
reply
236
views
EnhancedVolcano underrepresenting DEGs
R
updated 2 days ago by
Kevin Blighe
86k • written 4 days ago by
jabbari.parnian
▴ 30
4
votes
5
replies
1.7k
views
PyMOL: Gaps in protein structure yet shown by the sequence
PyMOL
structure
protein
updated 4 days ago by
pippo1980
• 0 • written 9 months ago by
spence.lank
▴ 10
0
votes
0
replies
111
views
[maftools]Too many multi_hit and missense mutation
maftools
gatk
MAF
data
WES
VCF
4 days ago by
jiazheng_lin
• 0
0
votes
1
reply
180
views
multiple condition and time course in RNA-seq
edgeR
RNA-Seq
DESeq2
updated 3 days ago by
i.sudbery
18k • written 4 days ago by
tiancaigg
▴ 30
0
votes
0
replies
124
views
Negative F statistics for sex check in plink
plink
check
sex
4 days ago by
kl
▴ 10
2
votes
4
replies
320
views
Should SMART-seq2 data be deduplicated in STAR?
SMART-seq2
4 days ago by
anlinli.napert
• 0
0
votes
3
replies
373
views
Extracting list of identical items from several excel files
from
excel
items
Extract
file
updated 4 days ago by
DonPhager
• 0 • written 5 days ago by
otieno43
▴ 20
1
vote
2
replies
260
views
Indexing by bowtie2 but aligning with STAR
STAR
mm10
Bowtie2
Alignment
Index
4 days ago by
Anojan
• 0
0
votes
1
reply
193
views
Chipseq peak calling and peak frequency region
chipseeker
macs2
updated 3 days ago by
Arup Ghosh
3.2k • written 5 days ago by
Mehwish
▴ 10
0
votes
3
replies
318
views
subset a bam file
bam
pysam
NGS
samtools
updated 5 days ago by
GenoMax
136k • written 5 days ago by
Ming
• 0
1
vote
1
reply
265
views
Forum:
want to work in open source project/project in bioinformatics
bioinformatics
project
updated 5 days ago by
Matthias Zepper
4.2k • written 5 days ago by
Afeef
• 0
0
votes
0
replies
171
views
Tutorial:
Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation
ggplotify
geom_tile
ggplot2
5 days ago by
rohitsatyam102
▴ 780
0
votes
1
reply
247
views
issue in RNA -seq analysis
NGS
RNA-Seq
updated 5 days ago by
GenoMax
136k • written 5 days ago by
subhiksha
• 0
2
votes
3
replies
1.0k
views
How to identify the 300 kb upstream and downstream genes of lncRNAs?
RNA-Seq
lncRNA
target genes
upstream
downstream
updated 6 days ago by
SeguraChain
• 0 • written 3.0 years ago by
mathavanbioinfo
▴ 70
4
votes
6
replies
545
views
BLAST hits on viruses relate to different host than used
Phage
BLAST
Metagenomics
5 days ago by
DonPhager
• 0
0
votes
3
replies
341
views
Alternatives to Music2 for rnaseq deconvolution without disease scRNA dataset
scRNA
deconvolution
Music
Music2
bulk
updated 5 days ago by
ATpoint
78k • written 6 days ago by
manuelmourato25
• 0
1
vote
4
replies
423
views
SNPs of a specific mouse strain
snp
updated 5 days ago by
Matthias Zepper
4.2k • written 7 days ago by
darklings
▴ 560
0
votes
0
replies
226
views
The number of variations in the pan-genome is reduced compared to the variations in the input VCF file
vg
6 days ago by
Wenke
• 0
0
votes
3
replies
301
views
Annovar - Annotated file cells show string
annovar
6 days ago by
Roshan
• 0
2
votes
6
replies
470
views
Genotypes in vcf files
genotypes
vcf
updated 6 days ago by
Jeremy Leipzig
22k • written 6 days ago by
amy__
▴ 160
1
vote
1
reply
210
views
Genetic data QC prior to imputation
imputation
updated 6 days ago by
Raony Guimarães
★ 1.3k • written 6 days ago by
kl
▴ 10
4
votes
2
replies
270
views
Excel Pasting Question
Excel
updated 6 days ago by
Pierre Lindenbaum
158k • written 6 days ago by
Bweil2
▴ 10
0
votes
1
reply
242
views
MinKNOW software installation doubt for MinION Nanopore sequencing
MinKNOW
MinION
Nanopore
updated 6 days ago by
GenoMax
136k • written 6 days ago by
Soumajit
▴ 40
0
votes
1
reply
214
views
htShinyExample-5.3 - not working
htShiny
Oncoprint
InteractiveComplexHeatmap
updated 1 day ago by
Ram
41k • written 6 days ago by
bioinfo
▴ 60
6
votes
5
replies
3.1k
views
Multi threading bowtie index
bowtie
indexing
updated 6 days ago by
colindaven
5.7k • written 8.2 years ago by
ChillarAnand
▴ 70
2
votes
4
replies
357
views
Human mitochondrial reference genome
reference
genome
mitochondria
2 days ago by
singhankit973
• 0
0
votes
0
replies
157
views
Seeking Advice on WGCNA for Nematode Sexual Dimorphism
WGCNA
Worms
RNA-Seq
6 days ago by
kdca
• 0
0
votes
3
replies
273
views
labelling the clusters from the CD4 T cell scRNAseq data
scRNAseq
6 days ago by
Sara
▴ 230
0
votes
0
replies
879
views
Any tools for finding the telomere sequences / lengths directly for nanopore sequencing reads without any prior knowledge of the organism
genomics
telomeres
reads
6 days ago by
Mark
• 0
1,000 results • Page
3 of 20
Recent Votes
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
Seurat integration of two datasets - GSE126783
about batch correction in scRNA-seq
How to compare two Seurat object (sample) in order to find top markers?
How do I resolve an integration error in Seurat?
The difference between merge and integration with Seurat objects
Analyzing single cell RNA seq with multiple samples and conditions
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Recent Replies
Comment: How can I map coordinates between two strains of yeast?
by
Jimmy
▴ 10
Yes (S. cerevisiae)
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
by
GenoMax
136k
> less than 100 for some samples Hmm. That is surprising but then in light of that fact ~20% recovery of cells does not sound bad.
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
by
newbee
▴ 40
Thanks for raising these valid points. I do not have the answer right now. Lately, I heard from the PI that they started with a small numbe…
Comment: How to get multiple protein domain database domain name from id's
by
GenoMax
136k
A list of InterPro domains is available: https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/entry.list
Answer: DIAMOND tutorial
by
GenoMax
136k
`DIAMOND` has a wiki page: https://github.com/bbuchfink/diamond/wiki Links for DIAMOND papers are here: https://github.com/bbuchfink/diamo…
Comment: How to do simple pathway analysis?
by
AK
★ 2.2k
Hi [he1k](https://www.biostars.org/u/139817/), Please use the following script which downloads and parses the keg data on the fly: [keg_hi…
Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison
by
CTLong
▴ 20
That's what I would assume, because we are not taking into account cross sample differences here. Thanks
Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison
by
CTLong
▴ 20
That's a good point. So its probably safest to not batch correct for within sample comparisons I guess?
Answer: Generating count matrix from Chromium Fixed RNA Profiling (FRP) data outside Cel
by
MohammadAlkadi
▴ 70
What is the purpose of doing so? I tried to do that by using the bam file generated by CellRanger. One **important detail** if you are work…
Comment: Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data
by
Kevin Blighe
86k
Thank you - appreciate the translation.
Answer: Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data
by
Kevin Blighe
86k
Em geral, uma taxa de descoberta falsa de 5% (p ajustado<0,05 ) deve ser usada para qualquer teste estatístico em que múltiplas hipóteses i…
Answer: WGCNA tutorial docs needed: Horvath Lab site down
by
ATpoint
78k
See link here from the developer: https://bioinformatics.stackexchange.com/a/21886/16676
Comment: WGCNA tutorial docs needed: Horvath Lab site down
by
Katie
• 0
I would also appreciate the PDFs if anyone has them please
Answer: Loftee no splice site annotations
by
AMARU
• 0
Hey, did you solve it? I am having a very similar issue. Thanks
Answer: Bulk and Single Cell RNA-seq online course
by
swbarnes2
13k
I'd start by getting tutorials for R libraries like DESeq, EdgeR, Seurat, etc, and learn by doing.
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