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121,198 results • Page
4 of 2424
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
238
views
Is there any way to treat antibody titers as continuous data for microbiome analysis?
antibody-titers
immunology
microbiome
19 days ago by
nmarin
• 0
55
votes
11
replies
49k
views
When and why is bwa aln better then bwa mem?
aln
comparison
bwa
mem
19 days ago by
dariober
15k
2
votes
1
reply
294
views
How to deal polyploid and aneuploid sugarcane genome R570 for variant calling
aneuploid
updated 17 days ago by
dthorbur
★ 3.0k • written 19 days ago by
analyst
▴ 60
2
votes
2
replies
336
views
False positives annotation of Augustus?
Augustus
training
updated 19 days ago by
lieven.sterck
15k • written 19 days ago by
Joseph
• 0
1
vote
2
replies
435
views
Mapping SNPs to genes
biomart
SNP
ensembl
r
gene
19 days ago by
Nigussie
• 0
0
votes
2
replies
320
views
Rockhopper Reference Genome Error
Rockhopper
19 days ago by
ATS
• 0
0
votes
0
replies
231
views
What can cause Faststructure to produce really high K clusters as optimal (e.g. 12 - 14)
SNP
vcf
population
19 days ago by
Drew
▴ 10
1
vote
7
replies
1.3k
views
Trouble finding datasets
GEO
SRA
updated 19 days ago by
ehaag
▴ 80 • written 19 months ago by
SHXVRR
▴ 20
4
votes
2
replies
1.1k
views
Imputation server failing to see samples in VCF files
imputation
VCF
updated 19 days ago by
Andresa Raquel Capodifoglio
• 0 • written 19 months ago by
Ben
▴ 10
0
votes
3
replies
368
views
Read Mapping of Reads to Reference Genome Shows Extreme Bias
mapping
read
bwa-mem
coverage
updated 19 days ago by
Michael
55k • written 19 days ago by
Lawrence
• 0
0
votes
0
replies
231
views
News:
Introduction to Python for Biologists (IPYB01)
Python
updated 19 days ago by
GenoMax
151k • written 19 days ago by
oliverhooker
▴ 110
0
votes
0
replies
229
views
News:
Machine Learning using Python (MLUP01)
Python
updated 19 days ago by
GenoMax
151k • written 19 days ago by
oliverhooker
▴ 110
2
votes
2
replies
333
views
Interpreting a vcf file
variant
vcf
updated 17 days ago by
cmdcolin
★ 4.2k • written 20 days ago by
ramiro.barrantes
▴ 20
3
votes
0
replies
274
views
Herald:
The Biostar Herald for Tuesday, April 29, 2025
herald
20 days ago by
Biostar
3.5k
5
votes
2
replies
437
views
Best choices for DGE and pathway enrichment analysis in single cell data using pseudobulk?
DEG
GSEA
single-cell
pseudobulk
17 days ago by
txema.heredia
▴ 210
6
votes
8
replies
2.7k
views
7 follow
Cluster annotation in single cell
Single-cell
updated 20 days ago by
Ethan
• 0 • written 20 months ago by
synat.keam
▴ 100
3
votes
6
replies
6.7k
views
Manual annotation of cell types in single cell RNA-seq
Seurat
single_cell
annotation
updated 20 days ago by
Ethan
• 0 • written 3.8 years ago by
Gene_MMP8
▴ 240
3
votes
7
replies
484
views
Clustal Omega stand alone versus website percent identity matrix
clustal
MSA
identity
percent
19 days ago by
sorrymouse
▴ 120
0
votes
1
reply
284
views
PCA vs sparse PCA : differences in results
ML
updated 20 days ago by
Ram
45k • written 20 days ago by
Ariadna
▴ 20
0
votes
1
reply
539
views
Is this the correct DESeq2 design for model with interaction terms and batch effect and paired samples?
paired
batch
DESeq2
interaction
updated 19 days ago by
ATpoint
88k • written 21 days ago by
vromman.marieke
• 0
0
votes
3
replies
2.4k
views
Has the TRON Expression Atlas closed?
RNA-Seq
cell-line
updated 21 days ago by
Adam
• 0 • written 6.0 years ago by
fracarb8
★ 1.7k
0
votes
0
replies
174
views
News:
online course: Machine Learning Methods for Longitudinal Data
R
LongitudinalData
Epidemiology
GeneExpression
Forecasting
21 days ago by
Physalia-courses
★ 2.6k
1
vote
3
replies
373
views
deseq2 batch effect correction
R
batch-effects
Deseq2
updated 10 days ago by
rfran010
★ 1.5k • written 21 days ago by
Devbio
• 0
2
votes
16
replies
938
views
How to generate identiy score between aligned sequences with Mauve?
identity
score
alignment
mauve
updated 14 days ago by
Charles Plessy
★ 2.9k • written 22 days ago by
marongiu.luigi
▴ 740
1
vote
3
replies
319
views
Error in deconvolution using CIBERSORTx
CIBERSORTx
deconvolution
updated 21 days ago by
Aspire
▴ 380 • written 21 days ago by
yadavsoumya647
• 0
3
votes
7
replies
1.5k
views
Tool:
A c library for reading and writing sequences in fasta and fastq format.
seqio
21 days ago by
dwpeng
▴ 120
0
votes
0
replies
206
views
pLoF variants for gnomAD v.4
gnomAD
pLoF
variants
grch38
21 days ago by
Damianos P. Melidis
▴ 40
0
votes
2
replies
364
views
Genomic Data Portal (GDC) download a given a link file
GDC
R
TCGA
TCGAbiolinks
maftools
updated 16 days ago by
Zhenyu Zhang
★ 1.3k • written 22 days ago by
bioinformagician
• 0
0
votes
1
reply
305
views
Finding matched RNA-seq and Ribo-seq datasets for Nicotiana benthamiana under the same condition
rna-seq
ribo-seq
translation-efficiency
dataset-search
nicotiana-benthamiana
updated 22 days ago by
colindaven
7.4k • written 23 days ago by
Farshid
• 0
3
votes
4
replies
636
views
Limma model gives weird results
model
multivariate
Limma
updated 23 days ago by
SamGG
▴ 150 • written 25 days ago by
leranwangcs
▴ 150
5
votes
5
replies
774
views
How to download the entire C. elegans genome from WormBase into Excel with automated gene descriptions
Gene
Wormbase
Celegans
20 days ago by
bioinformatics_rk
▴ 10
0
votes
0
replies
282
views
Job:
Postdoctoral Research Fellow, multi-omics, Univ of Nebraska Medical Center, Omaha, NE, USA
microbiome
Postdoc
metagenome
transcriptome
metabolome
updated 23 days ago by
GenoMax
151k • written 23 days ago by
era
• 0
0
votes
0
replies
266
views
How to deal with the clusterProfiler analysis result?
clusterProfiler
updated 23 days ago by
GenoMax
151k • written 23 days ago by
Tundup
▴ 10
0
votes
0
replies
298
views
News:
Genome Bioinformatics Summer School: OMICSS-25
training
bioinformatics
school
24 days ago by
Lilit
• 0
1
vote
2
replies
377
views
Unable to find mitochondrial genes in latest rat genome(GRCr8)
seurat
genome
mitochondrialgenes
NCBI
Singlecell
23 days ago by
dxj294
• 0
0
votes
0
replies
241
views
Haplotype reference for ShapeIt (ShapeIt5)
Phasing
24 days ago by
evan.kransdorf
• 0
6
votes
6
replies
522
views
Pre-Made STAR Index for mm10 Mouse Genome
STAR
updated 22 days ago by
colindaven
7.4k • written 24 days ago by
littlebioinformatician
• 0
1
vote
1
reply
321
views
The volcano plot shows data with an arm-shaped enrichment.
volcanoplot
updated 24 days ago by
ATpoint
88k • written 24 days ago by
lea.LD
• 0
0
votes
0
replies
256
views
Tool:
GENetLib: A Python Library for Gene–environment Interaction Analysis via Deep Learning
gene-environment
interaction
analysis
24 days ago by
Barry
• 0
9
votes
10
replies
761
views
STAR vs. Kallisto
STAR
kallisto
alignment
RNA-Seq
mapping
updated 20 days ago by
dsull
★ 7.5k • written 24 days ago by
gogeni5529
▴ 70
1
vote
1
reply
351
views
News:
Phylogenetic Comparative Methods in R (12–16 May, Online) - only 2 seats left
R
Phylogenetic-Comparative-Methods
12 days ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
325
views
Biostar handbook
Handbook
Biostar
updated 24 days ago by
GenoMax
151k • written 24 days ago by
himanshu0102
• 0
2
votes
2
replies
1.5k
views
pangenome - Create a diagram venn
roary
grep
awk
pangenome
venn
updated 24 days ago by
mplace
▴ 40 • written 2.1 years ago by
BATMAN
• 0
4
votes
4
replies
504
views
Addressing two nuisance factors in RNAseq
bulkRNAseq
updated 24 days ago by
ATpoint
88k • written 24 days ago by
jkim
▴ 190
1
vote
5
replies
613
views
DRAGEN FILTER
dragen
variant-calling
updated 25 days ago by
GenoMax
151k • written 25 days ago by
theresia.celine
▴ 10
1
vote
1
reply
477
views
Interpretation of the results: PCA
proteomics
PCA
21 days ago by
Ariadna
▴ 20
3
votes
5
replies
594
views
How to check normal BAM_files before create a Panel Of Normals (PoN)
GATK
variant_calling
PoN
25 days ago by
AIMAR
▴ 10
0
votes
1
reply
343
views
how to handle infinite M-values in methylation array data
M-value
methylation
infinite
array
updated 25 days ago by
Basti
★ 2.1k • written 25 days ago by
matt192
• 0
1
vote
3
replies
1.9k
views
Free and redistributable genomic data sets?
data
software-development
genomics
written 9.3 years ago by
woemler
▴ 170
3
votes
6
replies
1.3k
views
Rna-seq data
data
rna-seq
updated 19 days ago by
ehaag
▴ 80 • written 3.2 years ago by
biology_inform
▴ 60
121,198 results • Page
4 of 2424
Recent Votes
Answer: Longest Protein per Gene from gpff file
Comment: Cross-species differential gene expression, finding orthologs
Comment: CUT&Tag data processing: peak caller choice and typical peak size profile
A: Convert .Gff3 File To 12-Column .Bed File
A: Convert .Gff3 File To 12-Column .Bed File
Comment: Seeking Advice on Multisample Variant Calling Pipeline with BWA-MEME and GATK DR
Comment: DESeq2 outliers-should I be concerned?
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Recent Replies
Comment: Cross-species differential gene expression, finding orthologs
by
GenoMax
151k
> I'm using genome and gtf info that are publicly available to map and assemble the transcripts for all 3 species. Are you assembling the …
Answer: Longest Protein per Gene from gpff file
by
lieven.sterck
15k
Have a look ar [AGAT][1] , with special focus on the `agat_sp_keep_longest_isoform.pl` subcommand. You might first need to convert the gen…
Comment: Cross-species differential gene expression, finding orthologs
by
fe94
▴ 10
Thank you for the suggestion!! Yes cross-species DEG analysis, especially for non-model species, seems pretty tricky still.
Comment: Cross-species differential gene expression, finding orthologs
by
fe94
▴ 10
Hi GenoMax, I'm not sure I got your question right. I'm using genome and gtf info that are publicly available to map and assemble the trans…
Comment: PRS result interpretation
by
Sam
★ 4.8k
Currently, we still haven't figure out how to best use PRS on individual level. What are your research question? Why do you need to use a P…
Comment: How important are allele fractions when calling variants?
by
Jeremy Leipzig
23k
The allele fraction is the main thing but only after artefactual alignments have been removed. If the AF is .2 but the other .8 of reads sh…
Comment: Cross-species differential gene expression, finding orthologs
by
Madelaine Gogol
5.3k
I don't know that much about this area, but you might consider OMA instead or in addition to Orthofinder.
Answer: Modify read groups in BAM file
by
jkbonfield
★ 1.3k
As you're not modifying the records (the ID doesn't change), this is just a header change. Try `samtools reheader`. If you have a CRAM it…
Answer: Integration of NanoString CosMx FOVs
by
Bastien Hervé
6.3k
To have a more suitable answer to your question I would have a look at how the readout of RNA probes from CosMx is done. On the same run…
Comment: Unexpected negative correlation between gene-length and counts
by
Ben
▴ 20
Sorry, these were generated with EDASeq biasPlot() function. They are loess lines of log-counts against gene length. Yes each line is an i…
Comment: Cross-species differential gene expression, finding orthologs
by
GenoMax
151k
> differential gene expression across different species How many of these are you generating the data for yourself and how many are you g…
Comment: Fold change - a final explanation
by
Agnes
• 0
Hi, I'm trying to use limma to make a volcano plot for a continuous variable (i.e. AMH levels) for some proteomics data. For binary variabl…
Comment: DESeq2 outliers-should I be concerned?
by
ATpoint
88k
It means that DESeq2 has replaced outliers in 35 genes because they had a large Cook's distance and you had more than 7 replicates so a cer…
Answer: 9th Berlin Summer School in NGS Data Analysis 2025 (June 30 - July 4, 2025) -- S
by
ecSeq Bioinformatics
▴ 20
Almost full! Apply now if you still want to take part! First come, first served. [www.ecseq.com/summer-school][1] [1]: http:/…
Answer: Cross-species differential gene expression, finding orthologs
by
cfos4698
★ 1.1k
I faced this problem previously. While I can't comment here on the relevant merits of your suggested approach, I can outline what I did. In…
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