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122,012 results • Page
291 of 2441
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Votes
Replies
4
votes
2
replies
1.0k
views
paired test for differential expression on RNAseq data
differential-Gene-Expression
edgeR
RNA-seq
deseq2
R
updated 2.6 years ago by
Ram
45k • written 2.6 years ago by
minoo
▴ 10
0
votes
0
replies
929
views
Job:
Postdoctoral position in comparative cancer genetics in dogs at NMBU, Norway
dogs
cancer
genome
genomics
2.6 years ago by
Michael
56k
1
vote
0
replies
784
views
Explanation of vg deconstruct vcf output
vg_deconstruct
pggb
vg
vcf
pangenome
2.6 years ago by
lobinu
▴ 10
0
votes
0
replies
472
views
How to exclude readthrough gene after fusion detection
read-through
gene-fusions
2.6 years ago by
bio_elle
▴ 10
1
vote
1
reply
910
views
Testing Evolutionary Hypothesis ( branch-sites )
Evolutionary
ETE3
codeml
updated 2.6 years ago by
manaswwm
▴ 570 • written 2.6 years ago by
Juke34
9.3k
2
votes
2
replies
2.8k
views
Mapping IDs and file names from TCGA datasets
TCGA
updated 2.6 years ago by
Ram
45k • written 2.6 years ago by
Jaehyun
▴ 10
0
votes
2
replies
1.3k
views
CABSDock:fortran 2018 deleted feature
ubuntu
CABSDOck
fortran
updated 2.6 years ago by
GenoMax
154k • written 2.6 years ago by
Farha
• 0
0
votes
3
replies
1.6k
views
COG clustering
COG
updated 2.6 years ago by
moshi
▴ 150 • written 2.6 years ago by
Shweta
• 0
3
votes
2
replies
1.3k
views
High-resolution annotation of LTR elements
LTR
updated 2.6 years ago by
colindaven
8.0k • written 2.6 years ago by
liorglic
★ 1.5k
0
votes
3
replies
1.1k
views
Map barcode to gene
NGS
library
barcode
2.6 years ago by
Jinsoul
• 0
2
votes
2
replies
4.4k
views
bcftools annotate -a
bcftools
VCF
updated 2.3 years ago by
Ram
45k • written 2.6 years ago by
anasjamshed
▴ 140
2
votes
1
reply
1.7k
views
Understanding "drop-out" for scRNA-seq data
scRNA-seq
updated 2.6 years ago by
zdebruine
▴ 120 • written 2.6 years ago by
Alexander
▴ 220
5
votes
7
replies
4.1k
views
Overlay points with EnhancedVolcano R
RNAseq
EnhancedVolcano
volcano-plot
2.6 years ago by
redafazazi
▴ 30
0
votes
1
reply
832
views
Calculating Log of the odds (LOD) from Matrix eQTL output
QTL
matrixEQTL
updated 2.6 years ago by
LChart
5.1k • written 2.6 years ago by
vicky
▴ 30
1
vote
3
replies
1.4k
views
method for querying gnomAD with long list of "uncharacterized" variants
R
gnomAD
variant
GenomicRanges
updated 2.6 years ago by
Ram
45k • written 2.6 years ago by
Charles Murtaugh
▴ 50
3
votes
12
replies
6.5k
views
GATK Mutect2 tumor mode
gatk
mutect2
tumor
human
wgs
updated 2.6 years ago by
m. bioinfo
• 0 • written 5.1 years ago by
cocchi.e89
▴ 290
0
votes
5
replies
2.3k
views
Should I use TPM or TMM to plot gene expression boxplots in RNAseq?
RNASeq
TMM
DEG
TPM
DESeq2
updated 2.6 years ago by
i.sudbery
22k • written 2.6 years ago by
1215045934
▴ 80
0
votes
6
replies
2.0k
views
WGCNA goodGenes message error
goodGenes
WGCNA
updated 2.6 years ago by
andres.firrincieli
3.9k • written 2.6 years ago by
Lélé
▴ 10
0
votes
1
reply
911
views
Tool to identify mutations following global alignment?
Mutation
alignment
analysis
genomics
updated 2.6 years ago by
manaswwm
▴ 570 • written 2.6 years ago by
Mark
▴ 60
2
votes
3
replies
1.2k
views
I have a question for deg analysis tools
edgeR
DESeq
limma
DEG
ballgown
2.6 years ago by
likeabboo
• 0
0
votes
7
replies
3.1k
views
snpEff error when connecting to my built database
snpEff
2.6 years ago by
doggie
• 0
0
votes
2
replies
1.1k
views
DESeq2 replicates in time course data
replicates
time-course
DESeq2
updated 2.6 years ago by
Ram
45k • written 2.6 years ago by
fernando.perez8
• 0
0
votes
1
reply
590
views
poly A in paired end reads
polyA
paired-end
updated 2.6 years ago by
Ram
45k • written 2.6 years ago by
שיר
• 0
0
votes
0
replies
753
views
How to intuitively explain the Watterson Estimator without explaining the Coalescent?
genetics
population-genetics
genomics
2.6 years ago by
J.E.
• 0
0
votes
1
reply
891
views
how to analyse methylation data from GEO?
methylation
GEO
GEO2R
updated 2.6 years ago by
Basti
★ 2.1k • written 2.6 years ago by
BioNoobie
▴ 20
2
votes
1
reply
695
views
is this good atac seq counts
ATAC-seq
updated 2.6 years ago by
Ram
45k • written 2.6 years ago by
alwayshope
▴ 40
1
vote
2
replies
994
views
How can I find the frequency of the recognition sites found in the genome?
cut-frequency
restriction-enzymes
recognition-sequence
updated 2.6 years ago by
GenoMax
154k • written 2.6 years ago by
zpl015
• 0
2
votes
3
replies
2.8k
views
Can't add read group correctly to minimap2 sam alignmnet
group
read
GATK
minimap2
updated 2.6 years ago by
GenoMax
154k • written 2.6 years ago by
hans
▴ 20
0
votes
0
replies
653
views
Analyzing inter chromosomal interactions with count frequency using HiC data for Saccharomyces family
data
inter-chromosomal
HI-C
interactions
2.6 years ago by
chaimae_mr
• 0
2
votes
2
replies
978
views
BridgePRS
BridgePRS
PRS
2.6 years ago by
Mengna Zhang
▴ 10
1
vote
2
replies
1.0k
views
RNA seq analysis differential expression analysis
differentially-expressed-genes
RNA-seq
updated 2.6 years ago by
Ram
45k • written 2.6 years ago by
bioinformatics
▴ 60
3
votes
2
replies
827
views
use fastQC to get one summary report for all the multiple .gz files
fastQC
updated 2.6 years ago by
Ram
45k • written 2.6 years ago by
Kanishka
• 0
9
votes
11
replies
5.0k
views
Nextflow Singularity/Apptainer error: command not found
apptainer
singularity
nextflow
2.6 years ago by
Eliveri
▴ 350
1
vote
7
replies
4.0k
views
How to increase the speed of miRanda target prediction program?
miranada
mirna
parallel
updated 2.6 years ago by
kuttibiotech2009
▴ 30 • written 7.9 years ago by
lakhujanivijay
5.9k
3
votes
7
replies
2.3k
views
Downloading 3' UTR sequences for miRNA Target Prediction
utr
RNA-Seq
Assembly
sequence
genome
updated 2.6 years ago by
kuttibiotech2009
▴ 30 • written 5.7 years ago by
yronimuz
• 0
1
vote
5
replies
2.0k
views
bwa-meth unrecognized reference name during sam_parse
EM-seq
Methyl-seq
alignment
bwa-meth
2.6 years ago by
bp22
▴ 80
1
vote
1
reply
855
views
Fast mapping from PDB id to CATH domains
CATH
PDB
updated 2.6 years ago by
Mensur Dlakic
★ 30k • written 2.6 years ago by
jsylee0528
• 0
0
votes
2
replies
782
views
Running DESeq2 parallelized with pre-computed dispersions
deseq2
2.6 years ago by
ajay.g.nadig
• 0
6
votes
5
replies
4.1k
views
how to get around snakemake with different wildcards input to output rule
snakemake
2.6 years ago by
samuel
▴ 260
1
vote
1
reply
792
views
Specifying a variable as a random effect in model.matrix()
SNM
model.matrix
R
updated 15 months ago by
nhaus
▴ 420 • written 2.6 years ago by
Curious_Gene
▴ 10
4
votes
6
replies
1.5k
views
gff3 file format
gff3
genome
reference
updated 2.6 years ago by
GenoMax
154k • written 2.6 years ago by
bestone
▴ 30
0
votes
1
reply
1.6k
views
Job:
Full-Time Research Assistant Professor
Research
Assistant-Professor
updated 2.6 years ago by
Ram
45k • written 2.6 years ago by
Christi
• 0
3
votes
1
reply
851
views
analysing nanopore amplicon data
amplicon
genotyping
nanopore
ampliSAS
updated 2.6 years ago by
dthorbur
★ 3.1k • written 2.6 years ago by
khoojj
▴ 20
0
votes
0
replies
500
views
Differential Expression Analysis of single cell data with large difference in cell count for groups.
scRNA
seurat
DEG
2.6 years ago by
Saran
▴ 50
0
votes
4
replies
1.1k
views
Cutadapt using nano command
cutadapt
updated 2.6 years ago by
Mensur Dlakic
★ 30k • written 2.6 years ago by
machaalani29
• 0
0
votes
0
replies
609
views
News:
Course - INTRODUCTION TO THE ANALYSIS OF LONGITUDINAL DATA WITH R
Genomics
LongitudinalData
R
2.6 years ago by
Physalia-courses
★ 2.7k
4
votes
3
replies
1.4k
views
Differential expression vs tissue specific expression
RNAseq
DGE
tissue-specific
DESeq
updated 2.6 years ago by
ponganta
▴ 590 • written 2.6 years ago by
deman23
▴ 10
11
votes
11
replies
13k
views
Blog:
How to choose Normalization methods (TPM/RPKM/FPKM) for mRNA expression
mRNA-seq
gene-expression
normalization-methods
TPM
updated 2.6 years ago by
i.sudbery
22k • written 2.6 years ago by
Novogene
▴ 510
4
votes
3
replies
2.2k
views
Salmon TPM calculation constant
salmon
TPM
2.6 years ago by
shinyjj
▴ 60
2
votes
0
replies
1.0k
views
Herald:
The Biostar Herald for Tuesday, February 28, 2023
herald
2.6 years ago by
Biostar
3.6k
122,012 results • Page
291 of 2441
Recent Votes
Answer: Recommendations for 200 SNP markers genotyping
Comment: Reasonable number of SNPs in a bacterial genome.
The Biostar Handbook. A bioinformatics e-book for beginners.
Genome Assembly QC from BAM files
Answer: Scaling RNA-Seq data before clustering?
Answer: Scaling RNA-Seq data before clustering?
Online course: RNA sequencing data analysis using R and Bioconductor - 3–14 November
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Recent Replies
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine
by
Edward
• 0
Yes, we plan to make English the primary language of the Brave UI.
Comment: Reasonable number of SNPs in a bacterial genome.
by
michael.ante
★ 4.0k
If your bacterial species is a (human) pathogen, you might want to check outbreak analysis papers of that species. In general, you find t…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space?
by
lieven.sterck
16k
ok, missed that ... in any case that should not happen indeed. How did you determine that the files are not equal? I can indeed also see t…
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine
by
Ram
45k
Do you have a plan to make an English version of the UI?
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine
by
Edward
• 0
This can visualize the parameters of the generated workflow, software, and scripts, and manage the docker process of the script, software, …
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine
by
ATpoint
89k
Can you summarize in one sentence what the use case is? Is this a workflow manager?
Comment: Pseudogene - scarce info
by
ATpoint
89k
This reminds me strongly on my "masters" courses (doesn't deserve that name tbf). "Here is some poorly-described project with little to no …
Answer: scVI vs Harmony, which is better for cell type based clustering in brain tissue?
by
ATpoint
89k
There is no "better" is my experience. It always depends on the dataset. Try both and integrate your biological knowledge to decide which m…
Comment: DESeq2 on metagenome KO counts
by
Aleksandra
▴ 190
I just wrote that I misunderstood your initial question.
Comment: DESeq2 on metagenome KO counts
by
Aleksandra
▴ 190
What exactly did I not get?
Comment: Interpreting genomic features distribution for CUT&RUN peaks
by
rfran010
★ 1.7k
If I understand correctly, you see increased signal at TSS sites compared to control (taller peaks in browser). However, 92% of the 450 siS…
Comment: combine VCF from diploid reference/haplotypes for the same sample
by
cmdcolin
★ 4.3k
this question is a little similar to your previous question (https://www.biostars.org/p/9614638/). just as added info, here is a tool calle…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space?
by
aj123
▴ 130
As mentioned above, I just got the raw fastq files from the ftp site listed.
Comment: DESeq2 on metagenome KO counts
by
ATpoint
89k
This statement makes zero sense in response to what I wrote.
Comment: DESeq2 on metagenome KO counts
by
Aleksandra
▴ 190
I focused on the fact that DESeq2 models overdispersion, but overlooked its implicit assumption: normalisation works when the main source o…
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