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119,124 results • Page
2 of 2383
Sort: Rank
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Votes
Replies
0
votes
0
replies
178
views
Small rna library analysis
Sirna
small-rna
updated 3 days ago by
Ram
44k • written 3 days ago by
martta95
▴ 10
0
votes
0
replies
180
views
Statistical test to be used for dataset
biostatistics
statistical-test
updated 3 days ago by
Ram
44k • written 3 days ago by
odi
▴ 10
1
vote
2
replies
305
views
Questions Regarding Normalization and Standardization in RNA-seq Differential Analysis
RNA-seq
Normalization
updated 3 days ago by
Ram
44k • written 4 days ago by
wdasda122
▴ 10
0
votes
0
replies
169
views
News:
Online Workshop - A Practical Introduction to NGS Data Analysis (December 9-11, 2024)
Workshop
Variant-Calling
RNA-Seq
Illumina
DNA-Seq
updated 3 days ago by
Ram
44k • written 4 days ago by
ecSeq Bioinformatics
• 0
0
votes
0
replies
169
views
CNVKit batch output
CNVkit
deletion
duplication
4 days ago by
aLex97
• 0
0
votes
0
replies
176
views
IGV - Load custom variant track
vcf
igv
react
4 days ago by
sadapas
• 0
0
votes
1
reply
223
views
Why are the SINEs annotated as zero when using RepeatModeler + RepeatMasker?
SINEs
Repeatmodeler
RepeatMasker
updated 4 days ago by
Michael
55k • written 4 days ago by
mut
• 0
0
votes
0
replies
169
views
ucsc table browser
ucsc
4 days ago by
daffodil
▴ 10
1
vote
2
replies
653
views
Question about various of graph format. How to get the sequence and source of a specific node?
vg
3 days ago by
chuanj8848
• 0
0
votes
0
replies
169
views
Facing problems in analysis of bisulfite sequencing data
sequencing
Bisulfite
updated 4 days ago by
GenoMax
146k • written 4 days ago by
SHREYA
• 0
2
votes
2
replies
301
views
Can anyone share with me the R code for GSEA analysis?
R
code
GSEA
updated 4 days ago by
GenoMax
146k • written 4 days ago by
nuorain
▴ 30
0
votes
2
replies
294
views
extracting reads from FASTA/FASTQ file
RNA-seq
RNA
updated 4 days ago by
GenoMax
146k • written 4 days ago by
bleven
• 0
0
votes
3
replies
328
views
Different annotations for different isoforms from the same gene
metatranscriptomics
Trinity
RNA-seq
Isoform
updated 3 days ago by
Dunois
★ 2.6k • written 4 days ago by
Chikae
• 0
0
votes
0
replies
181
views
Forum:
epitope-TCR binding prediction, vaccine design
vaccine
epitope-TCR
binding
4 days ago by
Dara
• 0
0
votes
0
replies
207
views
Forum:
layoffs in biotech
layoff
biotech
4 days ago by
Dara
• 0
1
vote
1
reply
400
views
How to use lme4() to perform differential expression on bulk RNA seq data with multiple random effects?
bulkRNAseq
lme4
updated 4 days ago by
ATpoint
85k • written 4 days ago by
bioyas
▴ 20
0
votes
2
replies
282
views
Snakemake - pipeline shut down without error
snakemake
3 days ago by
bhumm
▴ 170
0
votes
1
reply
216
views
DeSeq2 filter transcripts
DeSeq2
RNA-seq
RNA
updated 4 days ago by
seidel
11k • written 4 days ago by
bleven
• 0
0
votes
0
replies
160
views
Setting up a case control with 18 VCFs in plink?
case-control
plink
WGS
4 days ago by
atopasn1
• 0
0
votes
1
reply
228
views
Aligning to transcriptome with STAR generates error in Salmon sequence length
STAR
Salmon
RNAseq
updated 4 days ago by
Dunois
★ 2.6k • written 4 days ago by
Lena
• 0
0
votes
1
reply
204
views
Gnomad result tables column meaning.
Gnomad
annotation
updated 4 days ago by
Pierre Lindenbaum
164k • written 4 days ago by
ijarne
▴ 10
1
vote
2
replies
283
views
DESeq2: adjusted p-values become NA when sub-setting samples
R
DEG
RNA-seq
DESeq2
updated 4 days ago by
GenoMax
146k • written 4 days ago by
txema.heredia
▴ 190
0
votes
1
reply
207
views
Trouble with Biopython residue depth
Proteins
Depth
Biopython
Residue
updated 4 days ago by
Wayne
★ 2.0k • written 4 days ago by
Anand KR
• 0
0
votes
2
replies
267
views
all genes have negative logFC edgeR
edgeR
updated 4 days ago by
rfran010
★ 1.3k • written 4 days ago by
xiaoyongli407
• 0
0
votes
2
replies
268
views
Split vcf file to fit tbi requirements
snp
HaplotypeCaller
vcf
gatk
9 hours ago by
cassandriatayfernandez
• 0
1
vote
0
replies
174
views
Dealing with indels in a fungal ITS2 MSA
indels
ITS2
MSA
alignment
5 days ago by
Sergio A.S.
▴ 10
0
votes
1
reply
235
views
GPU-accelerated multiple sequence alignment tools
Multiple-Sequence-Alignment
updated 4 days ago by
Ram
44k • written 5 days ago by
jet
• 0
2
votes
6
replies
567
views
WGCNA package.
RNA-seq
WGCNA
4 days ago by
Jaber
▴ 20
0
votes
3
replies
332
views
Question on batch effect for a bulk RNA seq analysis
RNA-seq
batch-effect
4 days ago by
akb
• 0
0
votes
0
replies
157
views
Paired splsda
splsda
updated 4 days ago by
Ram
44k • written 5 days ago by
michelafrancesconi9
▴ 20
0
votes
3
replies
258
views
Mapping to transcriptome without gtf annotation
transcriptome
Mapping
assembly
updated 5 days ago by
Michael
55k • written 5 days ago by
Biodee
• 0
0
votes
1
reply
212
views
Getting data from NCBI using Python
Ensembl
pyEnsembl
RNA-seq
updated 4 days ago by
Ram
44k • written 5 days ago by
Quân
• 0
2
votes
6
replies
1.3k
views
Mapping all 32-mers within Hamming Distance = 3
hamming
alignment
kmer
ngs
short
updated 4 days ago by
mourisl
▴ 30 • written 22 months ago by
giova34
▴ 10
0
votes
0
replies
151
views
How to work with Low allele Depth Variants in Strelka Variant caller
strelka
allelic-depth
low-GQX
updated 4 days ago by
Ram
44k • written 5 days ago by
abhishekghadge
▴ 30
0
votes
1
reply
861
views
What is the meaning of 'a too large, ITMAX too small in gamma countinued fraction (gcf)'
meta-analysis
METAL
GWAS
updated 5 days ago by
Ram
44k • written 19 months ago by
ymberzal
• 0
0
votes
0
replies
1.5k
views
METAL meta-analysis software crash
metal
meta-analysis
gwas
updated 5 days ago by
Ty
• 0 • written 4.5 years ago by
ydadmehr
• 0
1
vote
3
replies
254
views
cutadapt not working when calling in a bash code with qsub
qsub
trim
cutadpat
updated 5 days ago by
ATpoint
85k • written 5 days ago by
Meghan.T
• 0
2
votes
3
replies
250
views
Removing features from RNA assay in seurat
R
SEURAT
sc-RNA-Seq
updated 5 days ago by
yura.grabovska
▴ 530 • written 5 days ago by
Varun Gupta
★ 1.3k
0
votes
0
replies
116
views
News:
Eukaryotic Genome Assembly Using PacBio and Hi-C course (4-8 November)
Genome-Assembly
PacBio
Long-reads
Hi-C
5 days ago by
carlopecoraro2
★ 2.6k
0
votes
6
replies
982
views
miRNAseq - over-presented sequence in negative control
miRNAseq
adaptor
dimer
updated 5 days ago by
Ant
▴ 20 • written 13 months ago by
MH85
▴ 20
0
votes
0
replies
133
views
News:
Online Workshop - Bioinformatics Pipeline Development with Nextflow (November 13-15, 2024)
Workshop
Nextflow
RNA-Seq
5 days ago by
ecSeq Bioinformatics
• 0
0
votes
0
replies
121
views
Differential expression analysis from .chp files with Limma
expression
limma
IonTorrent
differential
5 days ago by
Rogerio Ribeiro
▴ 110
1
vote
2
replies
301
views
Genome Polishing nextPolish
nextpolish2
nextpolish
pilon
racon
4 days ago by
Umer
▴ 110
0
votes
1
reply
222
views
co-occurrence matrix from my VCF file
co-occurrence
vcf
updated 5 days ago by
robben
• 0 • written 7 days ago by
HarperReed
• 0
3
votes
6
replies
1.7k
views
Center multiple pheatmap
pheatmap
patchwork
updated 5 days ago by
yura.grabovska
▴ 530 • written 3.8 years ago by
5utr
▴ 370
5
votes
3
replies
308
views
creat histogram in R
R
ggplot2
hist
updated 6 days ago by
ATpoint
85k • written 6 days ago by
G.S
▴ 60
2
votes
5
replies
347
views
constructing gene-based pangenome from orthofinder output file
orthofinder
pan-genome
updated 5 days ago by
Dunois
★ 2.6k • written 6 days ago by
analyst
▴ 50
7
votes
6
replies
443
views
Genome Assembly Sorting
genome
assembly
sorting
updated 7 days ago by
GenoMax
146k • written 7 days ago by
Umer
▴ 110
0
votes
3
replies
361
views
Install PacBio lima via conda fails
conda
updated 6 days ago by
colindaven
6.8k • written 6 days ago by
michael.flower.14
▴ 200
1
vote
3
replies
282
views
human_variation_vcf
BaseRecalibrator
6 days ago by
runfreely2
• 0
119,124 results • Page
2 of 2383
Recent Votes
Answer: How to make DiffBind Run Faster?
Comment: Help on encode accessions
Answer: Modeltest-ng and MrBayes
Answer: Should I Learn Docker to Run Command Line Bioinformatics Tool?
A: Meaning of Chromatin state
Answer: Which Should Take Priority When Selecting DEGs: FDR or Log Fold Change?
A: MaxEntScan score interpretation
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Answer: Appropriate minimum gene set size for gene set enrichment analysis
by
yura.grabovska
▴ 530
This is very much an empirically defined parameter. It would make sense to benchmark within your data. Luckingly methods built on top of fg…
Comment: Help on encode accessions
by
GenoMax
146k
Data organization for ENCODE is described on this page: https://www.encodeproject.org/help/data-organization/
Comment: gtf files for various organism in ucsc
by
1769mkc
★ 1.2k
thank you for the insight i would give it a try and update
Comment: Choosing the best representative transcript for a gene
by
Michael
55k
There is no such thing as the best transcript, there is the possibility to select the longest transcript per gene from a transcriptome asse…
Comment: gtf files for various organism in ucsc
by
michael.ante
★ 3.9k
According to the description [here][1]: > refMrna.fa.gz - RefSeq mRNA from the same species as the genome. This sequence data is updat…
Comment: Seurat Xenium QC
by
Bastien Hervé
5.7k
You can check some papers using these technologies to see what QC they apply and would help you make your own for your dataset. The Seurat …
Comment: Unexplainable missing values in single cell Seurat object
by
Gerard
▴ 10
Oh, sorry. I created individual Seurat objects with Read10x (reading filtered matrixes) and CreateSeuratObject(min.cells = 3, min.features…
Comment: gtf files for various organism in ucsc
by
1769mkc
★ 1.2k
refMrna.fa.gz this contains the gtf? file i was expecting .gtf extension i will look for it.
Comment: Which Should Take Priority When Selecting DEGs: FDR or Log Fold Change?
by
bioinfo1994
▴ 10
Ah, I see it now! Thank you so much for taking the time to explain everything in such detail. I truly appreciate your help!
Comment: PCA for count data
by
QX
▴ 60
thank you!
Comment: cnvpytor run problem
by
yura.grabovska
▴ 530
I would definitely check if you're either running out of resources or if the server has specific rules for how jobs should be ran eg - queu…
Comment: PyMOL scripting with GPUs on LSF
by
GenoMax
146k
I don't see any mention of GPU support even with v.3.x: https://pymol.org/support.html?#installation
Comment: Does mageck-vispr calculate differently than mageck?
by
ATpoint
85k
But the mean-variance modelling is based on the normalized data (actually raw data corrected by size factors), so that comes after, no?
Comment: PCA for count data
by
Bastien Hervé
5.7k
I would do like it is done in single cell, where your `reg1,2,3` are cells and `a,b,c` are genes. You don't need to log transform your coun…
Comment: Unexplainable missing values in single cell Seurat object
by
Michael
55k
That would print a big mess on screen, but I don't get why there would be logical values instead of numeric values at all. Therefore, I wa…
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