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107,972 results • Page
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0
votes
0
replies
13
views
difference between chip-seq and association study
association
chip-seq
TWAS
1 hour ago by
rheab1230
▴ 120
0
votes
0
replies
19
views
Issues With Using Singularity In Order To Run Software "quested access to the resource is denied"
Singularity
2 hours ago by
Indira
• 0
0
votes
6
replies
1.2k
views
Gene trans map for Trinotate input using non-Trinity assembled transcriptome?
RNAseq
transcriptomics
Trinotate
assembly
annotation
updated 3 hours ago by
liyong
▴ 40 • written 12 months ago by
Corey
• 0
3
votes
4
replies
281
views
How to download all Gene Ontology (GO) IDs with their associated vocabulary?
download
GO
gene_ontology
updated 4 hours ago by
geneontologyhelp
▴ 150 • written 6 days ago by
Jimmy
• 0
716
votes
159
replies
104k
views
100 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
tutorial
News
handbook
updated 4 months ago by
Biostar
1.5k • written 6.2 years ago by
Istvan Albert
96k
0
votes
0
replies
30
views
gff2bed fails with "Non-numeric start coordinate. "
bedops
4 hours ago by
scottbrainard
▴ 50
0
votes
0
replies
34
views
Using bigWigCompare to correct for input signal
chip
input
peaks
bigwig
deeptools
4 hours ago by
Maycon
• 0
0
votes
0
replies
30
views
Tool to combine Germline Variant call from different variant callers
haplotypecaller
gatk
snps
4 hours ago by
rohitsatyam102
▴ 690
2
votes
2
replies
67
views
Creating reference genome that includes HIV genome
alignment
3 hours ago by
FrankStarling
▴ 20
0
votes
0
replies
29
views
Trying to understand the difference between between these two HGVS
hgvs
4 hours ago by
curious
▴ 720
0
votes
0
replies
32
views
RagTag patch error--"tuple index out of range"
correction
ragtag
scaffolding
5 hours ago by
schmiggle
• 0
1
vote
0
replies
47
views
Herald:
The Biostar Herald for Monday, February 06, 2023
herald
6 hours ago by
Biostar
1.5k
1
vote
2
replies
117
views
How to compare different illumina indices with each other to see how similar or different they are
alignment
sequencing
rna-seq
updated 6 hours ago by
GenoMax
125k • written 9 hours ago by
Apex92
▴ 260
0
votes
0
replies
48
views
network alignment and network regression
network
6 hours ago by
Bogdan
★ 1.3k
0
votes
0
replies
50
views
Can't convert paired end BAM to bed using bedtools
BAM
BEDPE
updated 6 hours ago by
GenoMax
125k • written 7 hours ago by
oksana03fel
• 0
0
votes
6
replies
277
views
how to get an average ROC curve after 10-fold cross validation in r
r
cross-validation
curve
roc
updated 1 hour ago by
Mensur Dlakic
★ 22k • written 1 day ago by
Lisa
• 0
0
votes
0
replies
50
views
Why does bcftools call from different max-depth (-d) value in mpileup give inconstant GT values?
mpileup
pileup
vcf
calling
bcftools
variant
7 hours ago by
magnolia
▴ 20
0
votes
1
reply
164
views
MetaboAnalyst: Interpreting Enrichment Analysis Results
enrichment
metabolomics
8 hours ago by
eva_u
▴ 10
0
votes
0
replies
42
views
Error: ##fileformat=VCFv4.2 does not exist
Pharmcat
VCF
8 hours ago by
taniamahmood38
▴ 20
1
vote
3
replies
101
views
Mapping with bbmap.sh
bbtools
SAM
bbmap
updated 7 hours ago by
GenoMax
125k • written 9 hours ago by
Hayler Edu
▴ 30
0
votes
0
replies
38
views
News:
Course - Version Control for Researchers
VersionControl
GIT
Github
9 hours ago by
carlopecoraro2
★ 2.2k
0
votes
3
replies
122
views
geom_errorbar not dodging or producing horizontal line
ggplot2
geom_errorbar
updated 6 hours ago by
FrankStarling
▴ 20 • written 9 hours ago by
bsp017
▴ 40
3
votes
5
replies
157
views
Size of two scRNA-Seq conditions
scRNA-Seq
7 hours ago by
Chris
▴ 60
5
votes
4
replies
148
views
What type of database does gnomAD use?
gnomAD
updated 9 hours ago by
Jeremy Leipzig
21k • written 13 hours ago by
Mariana Ribeiro
▴ 20
1
vote
2
replies
94
views
Dealing with missing (NA) values in my 450K methylation array dataset
minfi
PCA
expression
Methylation
R
5 hours ago by
Edward E-B
• 0
0
votes
1
reply
59
views
snp Caenorhabditis elegans
snp
Caenorhabditis-elegans
updated 10 hours ago by
Ram
37k • written 10 hours ago by
haiminabox
• 0
0
votes
1
reply
241
views
want the code for cuffdiff , NIOSeq , bayseq to perform DEGs.
DEGs
updated 10 hours ago by
4galaxy77
2.6k • written 3 days ago by
rupali
• 0
0
votes
0
replies
45
views
Mapping IDs to systematic names (GOSim, setevidencelevel() )
GOSim
updated 10 hours ago by
Ram
37k • written 11 hours ago by
eliska.ochodkova
• 0
0
votes
1
reply
72
views
Novogene somatic results with GATK mutect2
Mutect2
Novogene
GATK
somatic
VCF
updated 11 hours ago by
GenoMax
125k • written 13 hours ago by
chrisgr
▴ 20
2
votes
5
replies
168
views
fastqc: Per base sequence content
illumina
metagenomic
fastqc
7 hours ago by
khoojj
• 0
0
votes
0
replies
69
views
A question about Bioinformatik analysis and experimental design / comparing 2 experiments
DEseq2
Batch-effect
updated 10 hours ago by
Ram
37k • written 14 hours ago by
Frederik
• 0
4
votes
3
replies
105
views
Is it possible to do bedtools multicov across the entire genome?
bedtools
depth
hg38
14 hours ago by
amy__
▴ 50
0
votes
2
replies
145
views
Index with unmasked or masked in HISAT2
masked
HISAT2
toplevel
unmasked
6 hours ago by
ibq.enriquepola
• 0
2
votes
3
replies
179
views
How to enable multiple cores/threads for Bowtie2 or BWA using Macbook M2 chip?
mac
bowtie2
bwa
m2
updated 5 hours ago by
GenoMax
125k • written 17 hours ago by
weixiaokuan
▴ 130
1
vote
2
replies
255
views
Obtaining every"Protein ID" from a genome in OMA
OMA
orthologs
updated 14 hours ago by
Adrian Altenhoff
★ 1.0k • written 3 days ago by
christyh
• 0
0
votes
1
reply
111
views
Error, (in LoadSpliceMap) string to parse is too long
oma
LoadSpliceMap
omastandalone
orthology
updated 15 hours ago by
Adrian Altenhoff
★ 1.0k • written 22 hours ago by
ziqing
• 0
2
votes
1
reply
204
views
How to use CAFE from Orthofinder Results
expansion
orthofinder
cafe
gene
updated 16 hours ago by
dariober
14k • written 2 days ago by
ahmadjoyyia
▴ 10
0
votes
0
replies
82
views
Input data for LIMMA: unnormalised or vsn or other?
lima
normalisation
vns
16 hours ago by
Sebastian Hesse
▴ 320
0
votes
0
replies
69
views
question of exonerate output
protein
gff
exonerate
annotation
17 hours ago by
TN
• 0
2
votes
0
replies
90
views
CircRNA extraction from bulk RNA seq datasets using CIRCexplorer2 with STAR alignment
alignment
CIRCexplorer2
STAR
18 hours ago by
choijamtsm
▴ 60
1
vote
1
reply
200
views
Tripal installation question
BioDb
Drush
Tripal
Drupal
20 hours ago by
alslonik
▴ 260
2
votes
2
replies
255
views
Can Singularity be installed on a single-node server or does it have to be HPC?
Singularity
updated 22 hours ago by
tothepoint
▴ 720 • written 1 day ago by
SalmaElShafie
• 0
0
votes
0
replies
98
views
Mis-paired primers
amplicon
primers
Mis-paired
1 day ago by
Sara
▴ 10
0
votes
0
replies
87
views
show amplicon like exon in UCSC/IGV
amplicon
1 day ago by
Sara
▴ 10
0
votes
2
replies
163
views
scATAC-seq workflow
Signac
scATAC-seq
1 day ago by
bioinformatics.girl
• 0
0
votes
0
replies
121
views
Set Y limits for ggplot with sec.axis
rstudio
ggplot
1 day ago by
JirMan
• 0
0
votes
1
reply
125
views
Filter InterProScan output for a specific function
interproscan
annotation
updated 10 hours ago by
jv
▴ 800 • written 1 day ago by
Purger
• 0
0
votes
1
reply
152
views
f-index in treemix
treemix
introgression
f-index
1 day ago by
kk.mahsa
▴ 140
0
votes
2
replies
297
views
Network analysis for two Factors
score
protein
network
chip-seq
analysis
1 day ago by
Ankit
▴ 390
1
vote
2
replies
171
views
Virtual box
of
virtual
machine
Sleep
time
offtopic
updated 10 hours ago by
Ram
37k • written 1 day ago by
georgeof35
• 0
107,972 results • Page
1 of 2160
Recent Votes
Comment: How to compare different illumina indices with each other to see how similar or
A: Prepare gene families for CAFE
A: Prepare gene families for CAFE
Prepare gene families for CAFE
C: Seurat: Assay to use for differential expression in an integrated data
Answer: Creating reference genome that includes HIV genome
Answer: Creating reference genome that includes HIV genome
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Answer: Gene trans map for Trinotate input using non-Trinity assembled transcriptome?
by
liyong
▴ 40
This thread (https://github.com/Trinotate/Trinotate.github.io/issues/63) might helps.
Comment: how to get an average ROC curve after 10-fold cross validation in r
by
Mensur Dlakic
★ 22k
I have answered your questions at least once, and out-of-fold twice. It is up to you to read it, as there are only so many ways something c…
Answer: How to download all Gene Ontology (GO) IDs with their associated vocabulary?
by
geneontologyhelp
▴ 150
If anyone would like a less technical method, you can use an instance of InterMine and obtain this list in seconds. For example, use SGD's…
Comment: Creating reference genome that includes HIV genome
by
FrankStarling
▴ 20
Thanks @atpoint.
Answer: Creating reference genome that includes HIV genome
by
ATpoint
68k
Get both the human and viral genomes, both in fasta format, then use `cat` to combine both files. Technically speaking, in the merged genom…
Comment: Gene ontology with locus tags
by
sea.joson
▴ 10
Can you expound on creating a custom GO universe? Googling it didn't really yield too many hits. I do have a GFF file, but I still need to …
Comment: Gene ontology with locus tags
by
geneontologyhelp
▴ 150
This is the right idea. GO annotations describe the natural function of a particular gene, and therefore GO annotations are tied to gene p…
Comment: Dealing with missing (NA) values in my 450K methylation array dataset
by
Edward E-B
• 0
From that I get: > Error in svd(x, nu = 0, nv = k) : a dimension is zero
Comment: How to enable multiple cores/threads for Bowtie2 or BWA using Macbook M2 chip?
by
GenoMax
125k
`top` will show thread info but it will be aggregated in % (e.g. you will see 400% use for 4 cores). You could use `htop` to look at indivi…
Answer: How to compare different illumina indices with each other to see how similar or
by
GenoMax
125k
Using `bowtie` v.1.3.1 $ more inde >1 ACAGTGAT >2 ACTGATAG >3 ACTTGAGA >4 AGTCAATA >5 AGTTCCGG…
Comment: How to enable multiple cores/threads for Bowtie2 or BWA using Macbook M2 chip?
by
weixiaokuan
▴ 130
Thank you for your answer @GenoMax! Is there a way to dynamically monitor threads usage for a specific command such as bowtie2? I previous…
Comment: Index with unmasked or masked in HISAT2
by
ibq.enriquepola
• 0
I have read that in masked genomes low complexity and repetitive regions of DNA are detected and replaced with 'N', do you suggest using un…
Comment: how to get an average ROC curve after 10-fold cross validation in r
by
GenoMax
125k
Please do not post follow up information as `answers`. Use `ADD REPLY` or `ADD COMMENT`.
Comment: geom_errorbar not dodging or producing horizontal line
by
FrankStarling
▴ 20
ggplot(data2, aes(x=Cohort, y=Mean_R2, color = Trait)) + geom_errorbar(aes(ymin=Mean_R2+SD, ymax=Mean_R2-SD), position="dodge")+ …
Comment: Clustering and dynamic tree cutting
by
harish
• 0
thank you for the effort, I did calculate the hr as you have shown. hr <- hclust(as.dist(1-cor(t(scaledata), method="pearson")), method="c…
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