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
99 results • Page
2 of 2
Sort: Rank
Rank
Views
Votes
Replies
0
votes
4
replies
1.2k
views
Batch effects
Batch-effect
transcriptomics
updated 4 hours ago by
Ram
43k • written 2.6 years ago by
BioQueen
▴ 30
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 4 hours ago by
Ram
43k • written 3.7 years ago by
Lukadon77
• 0
0
votes
0
replies
713
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq
scRNA-Seq
batch-effect
updated 4 hours ago by
Ram
43k • written 3.4 years ago by
hkarakurt
▴ 180
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 4 hours ago by
Ram
43k • written 3.5 years ago by
oakhamwolf
▴ 20
0
votes
1
reply
794
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR
Batch-effect
RNA-Seq
updated 4 hours ago by
Ram
43k • written 3.7 years ago by
jordan15
• 0
2
votes
2
replies
1.0k
views
Batch correct batch 2 while leaving batch 1 unchanged.
limma
machine-learning
batch-effect
updated 4 hours ago by
Ram
43k • written 3.7 years ago by
i.sudbery
19k
0
votes
7
replies
1.8k
views
Batch effect correction in RNASeq data and plot Dendrograms cluster
clustering
dendrogram
RNA-Seq
batch-effect
updated 4 hours ago by
Ram
43k • written 4.0 years ago by
Ankit
▴ 500
22
votes
18
replies
6.1k
views
about batch correction in scRNA-seq
scRNA
scRNA-seq
batch-effect
updated 4 hours ago by
Ram
43k • written 4.5 years ago by
Bogdan
★ 1.4k
0
votes
0
replies
1.2k
views
Batch estimate using kBET
batch-effect
kbet
updated 4 hours ago by
Ram
43k • written 4.0 years ago by
getanid123
• 0
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 4 hours ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
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 4 hours ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
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 4 hours ago by
Ram
43k • written 4.5 years ago by
hkarakurt
▴ 180
2
votes
1
reply
2.1k
views
How to make batch univariate cox analysis for list
univariate-cox-analysis
updated 8 hours ago by
Ram
43k • written 4.8 years ago by
BioLite
▴ 20
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 8 hours ago by
colindaven
6.3k • written 10.9 years ago by
Ontheway
▴ 10
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat
RNA-Seq
Limma
DESeq2
batch-effect
updated 4 hours ago by
Ram
43k • written 4.9 years ago by
borkk
▴ 140
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 4 hours ago by
Ram
43k • written 5.0 years ago by
tigeradab
▴ 60
1
vote
4
replies
1.7k
views
Batch correction and DE analysis of miRNA Seq data
miRNAseq
Differential-Expression
batch-effect
updated 4 hours ago by
Ram
43k • written 5.0 years ago by
georgians
▴ 50
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 4 hours ago by
kjngo
• 0 • written 12.0 years ago by
Gabriel R.
★ 2.9k
0
votes
0
replies
1.7k
views
Differential expression using Scran batch corrected data
single-cell
Batch-effect
RNA-Seq
Scran
updated 4 hours ago by
Ram
43k • written 5.4 years ago by
baldissera152
▴ 10
0
votes
2
replies
1.2k
views
Normalization (microarray data)
microarray
Normalization
Batch-effect
updated 4 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 4 hours ago by
Ram
43k • written 6.5 years ago by
georgewwp
▴ 30
1
vote
0
replies
2.1k
views
Tool:
DASC -- detecting hidden batch effects in gene expression datasets (Array/RNA-Seq/scRNA-Seq)
RNA-Seq
scRNA-Seq
R
Batch-Effect
updated 4 hours ago by
Ram
43k • written 6.8 years ago by
Ar
★ 1.1k
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS
exome-sequencing
batch-effect
updated 4 hours ago by
Ram
43k • written 6.5 years ago by
Alternative
▴ 270
0
votes
1
reply
2.9k
views
Microarray batch effect correction
Microarray
Batch-effect
updated 4 hours ago by
Ram
43k • written 6.6 years ago by
sarahmanderni
▴ 100
0
votes
1
reply
1.8k
views
Advice required for remove batch effect which perfectly collinear with contrast of interest
RNA-seq
batch-effect
updated 4 hours ago by
Ram
43k • written 6.6 years ago by
boymin2020
▴ 80
2
votes
2
replies
1.8k
views
Time point microarray data correcting for batch effects
microarray
combat
batch-effect
updated 4 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 4 hours ago by
Ram
43k • written 6.8 years ago by
wamiqsaifi
• 0
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 4 hours ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
0
votes
0
replies
2.0k
views
NOISeq Batch Correction to RNA-seq data
Batch-effect
RNA-Seq
ARSyNseq
limma
NOISeq
updated 4 hours ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
1
vote
3
replies
2.0k
views
gene expression data analysis and batch effect methods
microarray
Gene-expression
batch-effect
updated 4 hours ago by
Ram
43k • written 6.9 years ago by
Shamim Sarhadi
▴ 220
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 4 hours ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 4 hours ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
6
votes
0
replies
2.5k
views
Tool:
Immuno-Navigator, a batch-corrected database for gene coexpression in the immune system
gene-co-expression
batch-effect
immunology
updated 4 hours ago by
Ram
43k • written 7.0 years ago by
alexis.vandenbon
▴ 80
1
vote
4
replies
3.1k
views
remove batch effect for multiple tumor data
RNA-Seq
batch-effect
updated 4 hours ago by
Ram
43k • written 7.1 years ago by
hellocita
▴ 40
0
votes
0
replies
1.9k
views
Correcting batch effect from known variables in RnBeads using Combat
Combat
450k
methylation
RnBeads
batch-effect
updated 4 hours ago by
Ram
43k • written 7.1 years ago by
rahel14350
▴ 40
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 4 hours ago by
Ram
43k • written 7.2 years ago by
tolgaturant
▴ 20
0
votes
0
replies
1.9k
views
batch effect in radseq
radseq
batch-effect
SNP
updated 4 hours ago by
Ram
43k • written 7.4 years ago by
oselm
▴ 50
1
vote
4
replies
13k
views
RNA sequencing data batch effect removal
RNA-Seq
batch-effect
updated 4 hours ago by
Ram
43k • written 7.4 years ago by
Tenghui Chen
• 0
0
votes
3
replies
3.2k
views
Batch correction (mass spectrometry data)
Combat
R
SVA
Biostatistics
batch-effect
updated 4 hours ago by
Ram
43k • written 7.4 years ago by
mkhadka10
• 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 4 hours ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 4 hours ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
2
votes
1
reply
2.3k
views
TCGA RNAseqV2 data matrix batch effect control and remove
RNA-Seq
batch-effect
updated 4 hours ago by
Ram
43k • written 7.6 years ago by
fractal61
▴ 10
3
votes
3
replies
2.9k
views
Quick way to Identify batch effect from covariates?
bioconductor
batch-effect
updated 4 hours ago by
Ram
43k • written 7.9 years ago by
James Ashmore
★ 3.4k
3
votes
2
replies
4.1k
views
Batch effects in sequencing data
batch-effect
updated 4 hours ago by
Ram
43k • written 8.7 years ago by
Andrew
▴ 60
0
votes
3
replies
3.0k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 4 hours ago by
Ram
43k • written 8.9 years ago by
siddharth.patel.153
• 0
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 4 hours ago by
Ram
43k • written 9.1 years ago by
chengzhao41
▴ 110
3
votes
8
replies
4.9k
views
An idea to identify batch effects
microarray
batch-effect
updated 4 hours ago by
Ram
43k • written 9.6 years ago by
mjarosz
• 0
9
votes
3
replies
6.9k
views
EdgeR-GLMs correcting for batch effects
RNA-Seq
edgeR
Batch-Effect
updated 4 hours ago by
Ram
43k • written 9.9 years ago by
Matina
▴ 250
1
vote
3
replies
3.3k
views
How to correct for batch effect in microarray meta-analysis
ComBat
microarray
meta-analysis
batch-effect
updated 4 hours ago by
Ram
43k • written 9.9 years ago by
BrunoGiotti
▴ 120
99 results • Page
2 of 2
Recent Votes
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Answer: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Recent Locations •
All
Russia,
just now
Spain,
2 minutes ago
Memphis, TN,
4 minutes ago
Canada,
6 minutes ago
Canada,
7 minutes ago
United States,
8 minutes ago
Belgium,
9 minutes ago
Recent Awards •
All
Commentator
to
GenoMax
141k
Centurion
to
jkbonfield
★ 1.2k
Popular Question
to
yueli7
▴ 250
Popular Question
to
Randy H
▴ 110
Popular Question
to
ManuelDB
▴ 80
Popular Question
to
lefthandgergo
▴ 10
Scholar
to
Juke34
8.5k
Recent Replies
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
Sure. Or, one could do: bash try.bash "Homo sapiens" AHR | xargs -I v_pdb curl -s -o v_pdb.pdb https://files.rcsb.org/view/v_pdb.pdb
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you so much
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
This may be the best option. Get the PDB ID's $ ./get.sh "Mus musculus" AHR 4M4X 5NJ8 5V0L 8H77 Then use `curl` to g…
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
It gives you the first 25 results though. I'll see if I can change that. EDIT: I've updated that number to 250. I'm hoping you won't need …
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you very much
Answer: Downloaded pdb's on rcsb.org
by
Ram
43k
I'm going to build off of OP's query and give them a simple script: ```bash organism=$(echo $1 | sed 's/ /%20/g') gene=$2 curl -s https:/…
Comment: miRNAs quantification using mirdeep2 tool
by
GenoMax
141k
This question does not make complete sense. If you have your own data files why do you need deep sequencing reads? Genome (can be download…
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
For a non-programmer using the search builder link included above may be the best option. Even that is not very user friendly.
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
That's how they seem to have written their query - automating that is a bit of a pain though as it takes a crazy JSON as input.
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
You can use the "Advanced query" builder (https://www.rcsb.org/search/advanced ) to create a query like: https://www.rcsb.org/search?requ…
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
PDB has a search API: https://search.rcsb.org/#search-example-1 Here's the JSON from your search query: ``` { "query": { "type": "grou…
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
Thank you very much. Actually I looked at there, but actually I want to find something like according to search url like this [QUERY: Gene …
Comment: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
BioinfGuru
★ 1.7k
great guidance ... thank you
Comment: error in CPC2
by
Ram
43k
Ashok, what is CPC2? Please edit your post and add as much context as you can.
Comment: python file for cpc2
by
Ram
43k
Ashok - someone else had to (guess and) add context to your post. Please give us as much information as you can in the first place - we can…
Traffic: 1942 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