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 : today
all time
today
this week
this month
this year
91 results • Page
1 of 2
Sort: replies
Rank
Views
Votes
Replies
22
votes
18
replies
6.1k
views
about batch correction in scRNA-seq
scRNA
scRNA-seq
batch-effect
updated 18 hours ago by
Ram
43k • written 4.5 years ago by
Bogdan
★ 1.4k
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 4 hours ago by
Hagen
▴ 10 • written 10.2 years ago by
filipzembol
▴ 180
11
votes
12
replies
714
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 13 hours ago by
Ram
43k • written 19 hours ago by
iamsmor
• 0
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 18 hours ago by
kjngo
• 0 • written 12.0 years ago by
Gabriel R.
★ 2.9k
2
votes
10
replies
604
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 20 hours ago by
GenoMax
141k • written 1 day ago by
me
• 0
9
votes
10
replies
6.8k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat
scRNA-seq
Harmony
RNA-seq
batch-effect
updated 17 hours ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
1
vote
9
replies
635
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 23 hours ago by
Elisabeth Gasteiger
★ 2.4k • written 1 day ago by
Jacky
• 0
3
votes
8
replies
4.9k
views
An idea to identify batch effects
microarray
batch-effect
updated 17 hours ago by
Ram
43k • written 9.6 years ago by
mjarosz
• 0
3
votes
8
replies
4.1k
views
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
fpkm
scRNA-seq
RNA-Seq
tpm
batch-effect
updated 17 hours ago by
Ram
43k • written 4.5 years ago by
hkarakurt
▴ 180
2
votes
7
replies
690
views
Removing duplicates
duplicates
ONT
minimap2
updated 13 hours ago by
joe
▴ 510 • written 2 days ago by
quentinperriere
• 0
0
votes
7
replies
1.8k
views
Batch effect correction in RNASeq data and plot Dendrograms cluster
clustering
dendrogram
RNA-Seq
batch-effect
updated 17 hours ago by
Ram
43k • written 4.0 years ago by
Ankit
▴ 500
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat
RNA-Seq
Limma
DESeq2
batch-effect
updated 17 hours ago by
Ram
43k • written 4.9 years ago by
borkk
▴ 140
2
votes
6
replies
5.1k
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 18 hours ago by
Ram
43k • written 3.7 years ago by
Lukadon77
• 0
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 21 hours ago by
colindaven
6.3k • written 10.9 years ago by
Ontheway
▴ 10
1
vote
4
replies
1.7k
views
Batch correction and DE analysis of miRNA Seq data
miRNAseq
Differential-Expression
batch-effect
updated 17 hours ago by
Ram
43k • written 5.0 years ago by
georgians
▴ 50
1
vote
4
replies
589
views
What happened to Tombo Re-squiggle
Tombo
resquiggle
ONT
updated 21 hours ago by
Ram
43k • written 3 months ago by
turcoa1
• 0
5
votes
4
replies
538
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq
EdgeR
DEGs
DESeq2
16 hours ago by
BioinfGuru
★ 1.7k
0
votes
4
replies
458
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
6 hours ago by
Kai Xin
• 0
2
votes
4
replies
6.0k
views
Batch Effect Removal in RNA-Seq Data for DGE & WGCNA. Should I omit any samples according to PCA plots?
Batch-effect
RNA-Seq
R
DESeq2
updated 17 hours ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
1
vote
4
replies
13k
views
RNA sequencing data batch effect removal
RNA-Seq
batch-effect
updated 17 hours ago by
Ram
43k • written 7.4 years ago by
Tenghui Chen
• 0
3
votes
4
replies
3.4k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 18 hours ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
1
vote
4
replies
3.1k
views
remove batch effect for multiple tumor data
RNA-Seq
batch-effect
updated 18 hours ago by
Ram
43k • written 7.1 years ago by
hellocita
▴ 40
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray
combat
batch-effect
median-normalization
updated 18 hours ago by
Ram
43k • written 17 months ago by
Dominique
• 0
1
vote
4
replies
1.4k
views
Removing/Accounting for batch effects in unbalanced group RNAseq data
rna-seq
batch-effect
deseq
updated 18 hours ago by
Ram
43k • written 2.2 years ago by
claysandel
• 0
0
votes
4
replies
1.2k
views
Batch effects
Batch-effect
transcriptomics
updated 18 hours ago by
Ram
43k • written 2.6 years ago by
BioQueen
▴ 30
3
votes
3
replies
371
views
Korean human genome reference file
GWAS
reference
imputation
8 hours ago by
SeoGyun
• 0
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 18 hours ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
0
votes
3
replies
343
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 13 hours ago by
swbarnes2
14k • written 1 day ago by
rrehimi
• 0
1
vote
3
replies
2.0k
views
gene expression data analysis and batch effect methods
microarray
Gene-expression
batch-effect
updated 18 hours ago by
Ram
43k • written 6.9 years ago by
Shamim Sarhadi
▴ 220
0
votes
3
replies
3.0k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 17 hours ago by
Ram
43k • written 8.9 years ago by
siddharth.patel.153
• 0
1
vote
3
replies
3.3k
views
How to correct for batch effect in microarray meta-analysis
ComBat
microarray
meta-analysis
batch-effect
updated 18 hours ago by
Ram
43k • written 9.9 years ago by
BrunoGiotti
▴ 120
3
votes
3
replies
3.0k
views
Quick way to Identify batch effect from covariates?
bioconductor
batch-effect
updated 17 hours ago by
Ram
43k • written 7.9 years ago by
James Ashmore
★ 3.4k
1
vote
3
replies
3.6k
views
Does Harmony batch correction for scRNA-seq require the same populations to be present in all samples?
Harmony
single-cell
scRNA-seq
batch-effect
updated 17 hours ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
7
votes
3
replies
2.6k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 5 hours ago by
colindaven
6.3k • written 15 months ago by
Dr.Animo
▴ 130
9
votes
3
replies
6.9k
views
EdgeR-GLMs correcting for batch effects
RNA-Seq
edgeR
Batch-Effect
updated 18 hours ago by
Ram
43k • written 9.9 years ago by
Matina
▴ 250
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 18 hours ago by
Ram
43k • written 3.5 years ago by
oakhamwolf
▴ 20
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 17 hours ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
0
votes
3
replies
3.2k
views
Batch correction (mass spectrometry data)
Combat
R
SVA
Biostatistics
batch-effect
updated 17 hours ago by
Ram
43k • written 7.4 years ago by
mkhadka10
• 0
2
votes
3
replies
364
views
Sheep reference genome remapping coordinates
reference
remap
sheep
coordinates
genome
23 hours ago by
valentinatsar
• 0
0
votes
2
replies
245
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
6 hours ago by
Ashok
• 0
2
votes
2
replies
344
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression
edgeR
20 hours ago by
nhaus
▴ 300
5
votes
2
replies
330
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
updated 20 hours ago by
shelkmike
★ 1.2k • written 1 day ago by
kirillkirilenko
▴ 40
0
votes
2
replies
1.2k
views
Normalization (microarray data)
microarray
Normalization
Batch-effect
updated 18 hours ago by
Ram
43k • written 6.3 years ago by
j_jamal96
▴ 20
4
votes
2
replies
3.7k
views
DESeq2 design and batch effect
RNA-Seq
batch-effect
DESeq2
Salmon
updated 18 hours ago by
Ram
43k • written 6.5 years ago by
georgewwp
▴ 30
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS
exome-sequencing
batch-effect
updated 18 hours ago by
Ram
43k • written 6.5 years ago by
Alternative
▴ 270
2
votes
2
replies
1.8k
views
Time point microarray data correcting for batch effects
microarray
combat
batch-effect
updated 18 hours ago by
Ram
43k • written 6.7 years ago by
tleona3
▴ 10
1
vote
2
replies
2.9k
views
Taking surrogate variable into account before running PCA
sva
svaseq
batch-effect
updated 18 hours ago by
Ram
43k • written 6.8 years ago by
wamiqsaifi
• 0
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 18 hours ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 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 18 hours ago by
Ram
43k • written 7.2 years ago by
tolgaturant
▴ 20
3
votes
2
replies
4.1k
views
Batch effects in sequencing data
batch-effect
updated 18 hours ago by
Ram
43k • written 8.7 years ago by
Andrew
▴ 60
91 results • Page
1 of 2
Recent Votes
Comment: Editing Human Reference Genome by adding a CDS
Answer: Plink merge errors.
Gene Set Enrichment Analysis
Gene Set Enrichment Analysis
A: Counting Number Of Bases In A Fastq File
Free/open source 23andme-like analysis
Comment: Free/open source 23andme-like analysis
Recent Locations •
All
France,
just now
United States,
just now
Tunisia,
1 minute ago
London, UK,
1 minute ago
Universe,
3 minutes ago
France/Nantes/Institut du Thorax - INSERM UMR1087,
4 minutes ago
Estonia,
7 minutes ago
Recent Awards •
All
Popular Question
to
i.sudbery
19k
Popular Question
to
biwdpang
• 0
Popular Question
to
Michael
54k
Scholar
to
Gordon Smyth
★ 7.0k
Popular Question
to
yueli7
▴ 250
Popular Question
to
Chirag Parsania
★ 2.0k
Scholar
to
LChart
3.9k
Recent Replies
Answer: Plink merge errors.
by
Dinmukhamed
• 0
I found answer https://www.biostars.org/p/101191/.
Comment: Ciriquant not configuring hisat2 indexed files
by
Atul K.
• 0
it worked. Thank you. Now my terminal is crashing, seems 16gb of RAM and 4 cores isn't enough. Can you suggest something?
Comment: Adding CB tag to bam file
by
Maria
• 0
I checked Picard ```AddOrReplaceReadsGroups``` and ```AddOATag```. Is that what you're referring to?
Comment: Free/open source 23andme-like analysis
by
Michael
54k
Noted that 'accurate' wasn't among your criteria ;) Anyway, most variant callers are free open-source software. However, for ancestry ana…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
by
Pierre Lindenbaum
161k
> server so I cannot use Blat for this purpose. blat is avilable as a standane tool: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
by
b.contreras.moreira
▴ 160
My favourite for this task would be [GMAP]( http://research-pub.gene.com/gmap ), which can produce GFF format with option `-f 2`. It is…
Answer: Prediction of Ribosomal RNA Genes Using RNAmmer Software
by
colindaven
6.3k
Another alternative is the truly free implementation barrnap https://github.com/tseemann/barrnap. This is also installable via conda so qui…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
by
Hagen
▴ 10
thanks! This saved me quite some time, I was about to write code to calculate the aligned length from the CIGAR. But this can be done with …
Comment: Per base sequence content failed miserably
by
Kai Xin
• 0
will look into that. Thank you very much
Comment: Korean human genome reference file
by
SeoGyun
• 0
Thanks..... But I want to do imputation, so I have to make it as a vcf file, but the site only has a fatsa file....
Comment: miRNAs quantification using mirdeep2 tool
by
Ashok
• 0
thank you for your reply https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md i saw this github tutorial for miRNA quantifica…
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
by
cmdcolin
★ 3.8k
Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
Comment: How to get the reference panel for UKBB
by
航太郎
• 0
Thanks for your guide!
Comment: Removing duplicates
by
joe
▴ 510
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis
by
swbarnes2
14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Traffic: 2369 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