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Limit : this year
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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
27
views
Annotating ENS codes to gene name
expression
RNA-seq
DEseq2
1 hour ago by
yoosefyud
▴ 40
0
votes
1
reply
69
views
HTSeq error processing GFF file
HTSeq
GFF
GTF
updated 2 hours ago by
barslmn
★ 1.2k • written 3 hours ago by
ibq.enriquepola
• 0
0
votes
0
replies
60
views
High downstream gene expression
downstream
High
Gene
expression
3 hours ago by
yoser4
▴ 10
0
votes
0
replies
42
views
which tool to use for Transposon structure finding CENSOR or repeat masker ??
transposon
DNA
repeat
CENSOR
masker
5 hours ago by
manaswiniparija3
▴ 10
0
votes
0
replies
48
views
scATAC merging of files
Signac
scATAC-seq
8 hours ago by
bioinformatics.girl
• 0
0
votes
0
replies
57
views
what does ALT ID DUP refer to when ALT ID for copy number are already specified
ALT
ID
CNV
VCF
10 hours ago by
anubratadas
▴ 20
0
votes
0
replies
73
views
How to use gseapy after scanpy?
gsea
single
cell
enrichR
gseapy
10 hours ago by
bioinfo
▴ 20
0
votes
0
replies
63
views
Trimmomatic
RNA
check
quality
fastaq
Trimmomatic
10 hours ago by
Monia
• 0
0
votes
0
replies
68
views
VNTR genotyping
NGS
VNTR
genotyping
11 hours ago by
Genotepes
▴ 950
0
votes
0
replies
65
views
Which AF column do I use from TCGA data in maftools
vcf2maf
sequencing
genome
WES
maf
12 hours ago by
CH1374
▴ 10
0
votes
0
replies
61
views
Chloroplast genome phylogenetic analysis
Inverted
region
Chloroplast
genome
Phylogenetic
analysis
SSC
12 hours ago by
a.bibek52
• 0
0
votes
0
replies
61
views
mVISTA annotation
alignment
Annotation
S-LAGAN
mVISTA
12 hours ago by
a.bibek52
• 0
2
votes
2
replies
134
views
Analyzing bulk RNA-seq
RNAseq
updated 11 hours ago by
swbarnes2
13k • written 14 hours ago by
Zaid
• 0
0
votes
13
replies
274
views
RNAseq for DE purpose
RNAseq
updated 11 hours ago by
swbarnes2
13k • written 14 hours ago by
m.habib
• 0
0
votes
0
replies
61
views
Identifying off-target mutation frequency in Bacterial genomes
dCas9-deaminase
off-target
SNPS
WGS
dCas9
15 hours ago by
pd378
• 0
0
votes
0
replies
53
views
SVA correction reduces ability to detect genes as differential expressed?
effects
RNAseq
expression
batch
SVA
gene
16 hours ago by
MB
▴ 50
0
votes
3
replies
159
views
CoveragePlot in Signac from MACS2 Object
Signac
scATAC-seq
updated 6 hours ago by
seidel
10k • written 16 hours ago by
bioinformatics.girl
• 0
0
votes
0
replies
74
views
Remove duplicates in multifasta, where entries are paired
bash
python
17 hours ago by
SaltedPork
▴ 170
1
vote
1
reply
94
views
snakemake Unexpected keyword bam in rule definition
snakemake
updated 15 hours ago by
Ram
37k • written 18 hours ago by
Aidand
• 0
0
votes
0
replies
58
views
Normalize Together Total RNA-SEQ vs Ampliseq protocols reads
RNA-seq
deseq2
ampliseq
ion-torrent
R
18 hours ago by
Fernando
• 0
0
votes
0
replies
63
views
Combining mRNA and total RNA studies
RNA-Seq
bulk
updated 15 hours ago by
Ram
37k • written 19 hours ago by
aksh
• 0
0
votes
0
replies
57
views
Twist Exome Sequencing Data: Palindromic Tandem Insertion-Deletion
NGS
Artefact
Twist
Sequencing
Exome
20 hours ago by
TraPS-VarI
• 0
0
votes
0
replies
112
views
Bootstrap in PhyML
phyml
bootstrap
22 hours ago by
Jimpix
▴ 10
0
votes
0
replies
96
views
Cibersort phenotpe file to create signature matrix
deconvolution
cibersort
file
phenotype
23 hours ago by
ce810b57
• 0
0
votes
0
replies
110
views
Enrichment map in python/ Pathway network by using python
interaction.
enrichment
network
pathway
analysis
1 day ago by
sonsunjirachote
• 0
0
votes
1
reply
152
views
How to analysis genomes with orthologs?
ortholog
genome
annotation
updated 21 hours ago by
GenoMax
125k • written 1 day ago by
沛煒
• 0
0
votes
0
replies
101
views
Does the falcon input CLR reads need corrected by Canu?
Genome
assemble
1 day ago by
leeunfeng
• 0
0
votes
0
replies
93
views
CUT&RUN H3K27me3 normalization with spike-in
deepTools
1 day ago by
mohansri1
• 0
0
votes
0
replies
106
views
How to identify nodes in a network with a higher degree and higher edge variance?
network
variance
WGCNA
igraph
updated 1 day ago by
ATpoint
68k • written 1 day ago by
adR
▴ 100
0
votes
2
replies
174
views
Can you apply Base Score Recalibration in parallel?
wgs
updated 1 day ago by
LChart
1.8k • written 1 day ago by
optimistsso4co3
▴ 100
0
votes
3
replies
234
views
Change accession number to chromosome number in reference genome
fasta
chromosome
updated 14 hours ago by
Ram
37k • written 1 day ago by
Tsigabu
• 0
0
votes
0
replies
80
views
Median depth across samples from multi-sample VCF
DP
bcftools
1 day ago by
alex.blakes
• 0
0
votes
5
replies
224
views
Add Information to Protein Fasta Headers
protein
fasta
functional-annotation
header
1 day ago by
ahmadjoyyia
• 0
3
votes
2
replies
154
views
WGCNA gene selection: gene significance or LASSO?
LASSO
WGCNA
updated 18 hours ago by
rpolicastro
11k • written 1 day ago by
janinubinu
• 0
0
votes
0
replies
82
views
count_matrix.csv generated by "prepDE.py3" script in Python3
Stringtie
RNA-seq
1 day ago by
Pegasus
▴ 40
0
votes
3
replies
251
views
biological vs. technical definition of "insert size"
grinder
simulated-reads
shotgun-sequencing
updated 1 day ago by
ATpoint
68k • written 1 day ago by
sovrappensiero
▴ 50
0
votes
0
replies
77
views
Haloplex HS - should you remove duplicates?
deduplicate
Haloplex
duplicates
1 day ago by
amy__
▴ 50
0
votes
0
replies
82
views
Interpreting SnpEff output plots
NGS
Annotation
SnpEff
WGS
WES
1 day ago by
Alireza
▴ 20
0
votes
0
replies
75
views
Using DANPOS2 to determine nucleosome positions
MNase-seq
DANPOS
ENCODE
bigwig
1 day ago by
elisheva
▴ 120
0
votes
0
replies
82
views
How to determine the receptor and binding site of a protein transcribed from a gene
gene
1 day ago by
yoser4
▴ 10
0
votes
3
replies
151
views
blast engine error empty blast query vector
error
alignment
Blast
updated 1 day ago by
pbioinf
▴ 30 • written 1 day ago by
Sowmya Pulapet
▴ 10
0
votes
0
replies
93
views
WGCNA Error in moduleEigengenes: setting key from pcagrey to pcagrey_
wgcna
1 day ago by
瀚
• 0
0
votes
0
replies
96
views
Exon 1 coverage of ADAMTS2 gene
WGS
Coverage
2 days ago by
ramya
• 0
0
votes
0
replies
110
views
bcftools error: bcftools could not parse pval threshold loidly
bcftools
mpileup
2 days ago by
mut.patricia
▴ 20
0
votes
0
replies
129
views
How to show the correlation between the expression of one gene and all the cell miRNAs expression levels?
expression
miRNA
correlation
2 days ago by
Zahra
▴ 90
0
votes
2
replies
165
views
No variants found ( have problem in the handbook)
bcftools
handbook
variation_calling
igv
1 day ago by
quanyu
• 0
0
votes
0
replies
124
views
Anti-CRISPR and Cas protein interactions
crispr
anti-crispr
proteins
updated 2 days ago by
GenoMax
125k • written 2 days ago by
Moein
• 0
0
votes
0
replies
125
views
issues with amber_minimize.py failing to use CUDA within alphafold
linux
CUDA
amber
alphafold
2 days ago by
charlieclark1ee
▴ 10
1
vote
1
reply
154
views
tools that align sequences in mouse and human
r
updated 2 days ago by
dthorbur
▴ 260 • written 2 days ago by
Chironex
▴ 40
0
votes
0
replies
119
views
Database of Embryo-Lethal or Known Knockout Phenotype Genes in Rice
annotation
database
rice
gene
2 days ago by
sviatoslav.kendall
▴ 840
1,000 results • Page
1 of 20
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Answer: 'SyntaxError': 'return' outside function?
Comment: Analyzing bulk RNA-seq
The Biostar Handbook. A bioinformatics e-book for beginners.
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Comment: How to extract the list of genes from TCGA CNV data
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Unfortunately it seems that *gaia* has been deprecated. You could still try to install a previous version of it, or set up a new conda envi…
Comment: RNASeq differential expression masked by pathways disregulation
by
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68k
If this is the case then you cannot correct for anything as this effect is nested with center.
Comment: HTSeq error processing GFF file
by
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★ 1.2k
That error message is very descriptive. Could you also add the line 997531?
Comment: RNASeq differential expression masked by pathways disregulation
by
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▴ 110
Thanks for the answer. However I am not sure this could be considered batch since CC2 samples have true upregulation of specific pathways t…
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Hello #gubrins Have you found the answer
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10k
The `object` will the the Seurat object you're working with, because that contains the data that will be plotted (Tn5 insertion events per …
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Using [**Entrezdirect**][1]. Date in last column is collection date. No way to query using it though. Could be wrong. $ esearch -db nu…
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Mensur Dlakic
★ 22k
Pretty sure that nothing other than HHsuite outputs results in `.hhr` format.
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Same allele = weight of 1, different allele = weight of 0. You can read more here: https://choishingwan.github.io/PRS-Tutorial/plink/#gener…
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Hi jv, Thank you for your help. But I am still uncertain. The GSEA tools can process the preranked list. However, it still required that I…
Answer: 2D structure of a custom protein (not in any databases) from a PDB file.
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Jiyao Wang
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You can also try out [iCn3D](https://structure.ncbi.nlm.nih.gov/icn3d). After you load your custom PDB via the menu "File > Open File > PDB…
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by
bioinformatics.girl
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What is 'peaks' entered as?... The input is: CoveragePlot( object = pbmc, region = "CD8A", ranges = peaks, …
Comment: Faking hh-suite workflow / alignment output
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I totally get your point, maybe long-winded was also not the right description for my issue. One example, [custom databases][1] are very cl…
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Wouldn't you take your MACS2 files, import them with rtracklayer so that they are GRanges objects, and then pass those as the peaks? i.e. w…
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Honestly, I think most RNASeq aligners are fairly robust to adapters. You could probably get away with not trimming at all
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