Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this month
all time
today
this week
this month
this year
897 results • Page
6 of 18
Sort: Votes
Rank
Views
Votes
Replies
2
votes
2
replies
1.7k
views
Remove batch effect for many RNA-seq
ComBat
RNA-Seq
batch-effect
sva
updated 28 days ago by
Ram
43k • written 4.8 years ago by
Shaway
• 0
2
votes
3
replies
841
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 11 days ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
2
votes
2
replies
248
views
STRING-DB API can't find my protein but I can find it when I go to the STRING-DB website directly
STRING-DB
protein
STRING-DB-API
10 days ago by
brandon
• 0
2
votes
9
replies
936
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 22 days ago by
LauferVA
4.2k • written 7 months ago by
Gnana
• 0
2
votes
4
replies
2.3k
views
Negative values after batch correction using removeBatchEffect from Limma
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 29 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
2
votes
4
replies
2.7k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel
gatk
calling
snp
variant
updated 16 days ago by
Medhat
9.7k • written 2.0 years ago by
Vitor1
▴ 120
2
votes
5
replies
532
views
Marking duplicates using UMIs
Deduplication
UMI
updated 24 days ago by
i.sudbery
19k • written 25 days ago by
Lipika
• 0
2
votes
1
reply
337
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun
metagenomics
blastp
taxonomy
updated 26 days ago by
GenoMax
142k • written 26 days ago by
rebecca.calvo
• 0
2
votes
4
replies
719
views
Count all variants from vcf file
variants
vcf
Count
updated 9 days ago by
Pierre Lindenbaum
161k • written 21 months ago by
t.ali
• 0
2
votes
2
replies
646
views
Batch correction for DE analysis
batch-correction
mRNA
RNA-seq
DEGs
MDSplot
updated 29 days ago by
Ram
43k • written 2.7 years ago by
Yoonji
▴ 10
2
votes
3
replies
322
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 12 days ago by
dthorbur
★ 2.0k • written 13 days ago by
Vijith
▴ 30
2
votes
4
replies
5.6k
views
44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped reads with STAR
rna-seq
alignment
RNA-Seq
featureCounts
STAR
updated 2 days ago by
Thind amarinder
▴ 340 • written 4.9 years ago by
garbuzov
▴ 70
2
votes
1
reply
329
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 12 days ago by
chrchang523
10k • written 16 days ago by
8armed
▴ 10
2
votes
6
replies
368
views
BWA alignment
Samtools
bam
updated 1 day ago by
a.alnawfal.1992
▴ 260 • written 3 days ago by
Vahid
• 0
2
votes
3
replies
205
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 1 day ago by
Ram
43k • written 1 day ago by
Prawesh
• 0
2
votes
5
replies
403
views
Importing a fastq file
Fastq
updated 6 days ago by
size_t
▴ 120 • written 7 days ago by
oumo
• 0
2
votes
6
replies
3.8k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell
RNAseq
DE Analysis
Treatment
Control
updated 20 days ago by
ATpoint
82k • written 3.9 years ago by
grayapply2009
▴ 280
2
votes
7
replies
1.4k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 17 days ago by
Gordon Smyth
★ 7.2k • written 8 months ago by
Calum
▴ 10
2
votes
5
replies
2.9k
views
Batch effect in Axiom Human Origins Array
affymetrix
array
batch-effect
updated 29 days ago by
Ram
43k • written 7.9 years ago by
Simo
▴ 50
2
votes
5
replies
783
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 25 days ago by
Jesse
▴ 770 • written 26 days ago by
Ann
★ 2.4k
2
votes
5
replies
422
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
20 days ago by
Lada
▴ 30
2
votes
4
replies
372
views
SnpEff annotates coding duplication as intronic?
snpeff
29 days ago by
kirill.zaslavsky
• 0
2
votes
1
reply
231
views
Failed to open VCF file
GATK
sentieon
BWA-MEM
updated 5 days ago by
Pierre Lindenbaum
161k • written 5 days ago by
melissachua90
▴ 70
2
votes
2
replies
305
views
p-value in CIBERSORT
CIBERSORT
p-value
15 days ago by
michelafrancesconi9
▴ 20
2
votes
4
replies
389
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 22 days ago by
swbarnes2
14k • written 23 days ago by
dxj294
• 0
2
votes
2
replies
1.6k
views
Combining control samples from 2 separate studies. Model matrix for batch effect?
gene-expression
R
limma
batch-effect
model-matrix
updated 27 days ago by
Ram
43k • written 7.3 years ago by
tolgaturant
▴ 20
2
votes
3
replies
270
views
Finding variants within a subset of a BAM file
variant
calling
1 day ago by
ramiro.barrantes
• 0
2
votes
3
replies
379
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 23 days ago by
Mensur Dlakic
★ 27k • written 23 days ago by
emmanouil.a
▴ 120
2
votes
6
replies
5.3k
views
How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?
scRNA-seq
R
seurat
harmony
batch-effect
updated 27 days ago by
Ram
43k • written 3.8 years ago by
Lukadon77
• 0
2
votes
4
replies
408
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
22 days ago by
HyperEvo
• 0
2
votes
5
replies
631
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis
MEGA
updated 25 days ago by
Mensur Dlakic
★ 27k • written 26 days ago by
Giorgio
• 0
2
votes
5
replies
2.5k
views
identifying transgene insertion site in WGS
WGS
insertion site
trangene
de-novo
soap
updated 7 days ago by
Cameron.walker9900
• 0 • written 5.1 years ago by
Assa Yeroslaviz
★ 1.8k
2
votes
1
reply
2.1k
views
How to make batch univariate cox analysis for list
univariate-cox-analysis
updated 27 days ago by
Ram
43k • written 4.8 years ago by
BioLite
▴ 20
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 15 hours ago by
Ram
43k • written 3.9 years ago by
millere
• 0
2
votes
2
replies
295
views
How to filter columns in a raw sparse matrix in R
matrix
R
updated 29 days ago by
bk11
★ 2.4k • written 29 days ago by
bgbs
• 0
2
votes
2
replies
215
views
MA plot of shrunken fold change
MA-plot
Deseq2
updated 16 days ago by
ATpoint
82k • written 16 days ago by
Sudip
• 0
2
votes
8
replies
359
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 3 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
Matteo Ungaro
▴ 100
2
votes
3
replies
1.5k
views
RNASeq - How to compare the expression of a single gene across batches
RNA-Seq
edgeR
batch-effect
updated 27 days ago by
Ram
43k • written 3.6 years ago by
oakhamwolf
▴ 20
2
votes
0
replies
154
views
News:
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics
SNPs
LocalAdaptation
GIS
6 days ago by
carlopecoraro2
★ 2.5k
2
votes
5
replies
258
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 2 days ago by
Philipp Bayer
8.5k • written 2 days ago by
林明德
• 0
2
votes
4
replies
282
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
1 day ago by
Esraa
• 0
2
votes
2
replies
240
views
Raw counts using stringtie
stringtie
RNA-seq
updated 12 days ago by
GenoMax
142k • written 12 days ago by
ahmad.sajad4541
• 0
2
votes
2
replies
1.1k
views
Can we directly use batch corrected gene expression (Bulk RNA-seq) for further downstream analyses?
RNA-Seq
batch-effect
updated 27 days ago by
Ram
43k • written 5.1 years ago by
tigeradab
▴ 60
2
votes
3
replies
498
views
Sheep reference genome remapping coordinates
reference
remap
sheep
coordinates
genome
28 days ago by
valentinatsar
• 0
2
votes
2
replies
426
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression
edgeR
27 days ago by
nhaus
▴ 360
2
votes
5
replies
564
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
29 days ago by
Bikram Kumar
• 0
1
vote
4
replies
183
views
Annotating file using bcftools
annotation
plink
bcftools
updated 3 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
kl
▴ 10
1
vote
0
replies
248
views
Job:
CTO/founding engineer role at Voyant Bio
engineer
20 days ago by
Assaf
▴ 10
1
vote
5
replies
368
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
13 days ago by
Riccardo
▴ 10
1
vote
1
reply
205
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 29 days ago by
dsull
★ 6.0k • written 29 days ago by
niruf
• 0
897 results • Page
6 of 18
Recent Votes
MAFtools variant classes mapping
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
A: How to process (seems) Agilent microarrry data?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
A: How To Merge Two Fastq.Gz Files?
Answer: Annotating file using bcftools
Recent Locations •
All
Spain,
just now
Germany,
just now
Bologna,
2 minutes ago
Morocco,
2 minutes ago
Perth, Australia,
2 minutes ago
Portugal,
3 minutes ago
United States,
3 minutes ago
Recent Awards •
All
Popular Question
to
Jalil Sharif
▴ 80
Popular Question
to
biology_inform
▴ 50
Scholar
to
nd48
▴ 20
Teacher
to
aw7
▴ 300
Supporter
to
thereallbaker
• 0
Popular Question
to
Apprentice
▴ 160
Teacher
to
ATpoint
82k
Recent Replies
Comment: Can I perform a correlation test with 3 biological replicates per condition?
by
ATpoint
82k
You're welcome. Yes, unfortunately you need quite a sample size for WGCNA simply because correlations with few samples are vastly underpowe…
Comment: Can I perform a correlation test with 3 biological replicates per condition?
by
manuelmourato25
• 0
Ah, I see. So seen that what I want is the per-gene correlation, the minimum of 20/25 for the pearson correlation still applies. Thank you …
Answer: Can I perform a correlation test with 3 biological replicates per condition?
by
ATpoint
82k
I think you're misunderstanding some concepts here. WGCNA is a framework that defines modules based on how and which genes are correlated …
Comment: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
by
GenoMax
142k
> most up-to-date build Major build of the genome remains GRCh38. What you are looking at is the latest patch release for that build. Only…
Comment: Can I perform a correlation test with 3 biological replicates per condition?
by
manuelmourato25
• 0
Thank you @atpoint . My apologies, maybe I should rephrase the question. I read the WGCNA docs already, and for the Pearson correlation tes…
Comment: How to extract cells of different species after mapping with combined genome?
by
GenoMax
142k
Can you confirm that this answer is specific for `singleron` technology and associated bioinformatics software.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
What OS are you using? Are you able to run `blastn --help` and does it produce the in-line help? > I used many query file.fasta And tho…
Comment: Can I perform a correlation test with 3 biological replicates per condition?
by
ATpoint
82k
> However, even though 3 biological replicates per condition seems to be the norm in these experiments, many papers discuss that we need at…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
ATpoint
82k
> I have curiosity, why do you make a desing with interceptor and without contrast matrix? Because for a 2-group comparison you do not nee…
Comment: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
by
ATpoint
82k
If you have a one-click workflow ready and the necessary computation power to casually run it, then go for it. If it is any greater effort …
Comment: Seurat v5 and how to correctly integrate across multiple experiments
by
Papyrus
★ 2.9k
In my experience integration methods are also often used for different samples/batches across the same technology. The crucial thing is to …
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
Thank you very much! I have repeated the code adding arrayWeights() and it's works! In this case, I have a desing without intercept and c…
Comment: Is there any way to modify this pie chart ?
by
ohtang7
▴ 40
Thank you, I've tried but I see only some appear in the chart in wrong segments. Could you help me to solve this how ? ![enter image desc…
Comment: perseus software (version 1.5.5)
by
DGTool
▴ 10
If the tool mentioned relates to the Perseus application from the Cox lab ([here][1]), it should be free to download after accepting the li…
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
by
DGTool
▴ 10
At least so far to my knowledge, I don't think it would be worth re-mapping to GRCh38.p14, if it is too much trouble or with what you're lo…
Traffic: 2697 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6