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
1,000 results • Page
1 of 20
Sort: Views
Rank
Views
Votes
Replies
164
votes
70
replies
61k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
fastq
next-gen-sequencing
updated 29 days ago by
Ram
43k • written 12.8 years ago by
Panos
★ 1.8k
98
votes
106
replies
46k
views
26 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 18 days ago by
psb7
▴ 20 • written 5.7 years ago by
Kevin Blighe
87k
39
votes
9
replies
42k
views
6 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 10 days ago by
Ram
43k • written 6.7 years ago by
lessismore
★ 1.3k
103
votes
42
replies
31k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 18 days ago by
Jeremy Leipzig
22k • written 10.5 years ago by
14134125465346445
★ 3.6k
57
votes
22
replies
28k
views
7 follow
Batch correction in DESeq2
Combat
DESeq2
Batch-Effect
updated 21 days ago by
Ram
43k • written 4.5 years ago by
Arindam Ghosh
▴ 510
22
votes
14
replies
28k
views
7 follow
removing batch effects using ComBat and SVA
SVA
ComBat
R
Batch-effect
updated 18 days ago by
Ram
43k • written 7.9 years ago by
LJ
▴ 280
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 8 days ago by
kjngo
• 0 • written 12.0 years ago by
Gabriel R.
★ 2.9k
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 9 days ago by
Gordon
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.2k
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 7 days ago by
Hagen
▴ 10 • written 10.2 years ago by
filipzembol
▴ 180
81
votes
27
replies
20k
views
12 follow
ATAC-seq sample normalization
ChIP-Seq
atac-seq
normalization
updated 23 days ago by
sgv
• 0 • written 4.3 years ago by
Flo
▴ 240
76
votes
72
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
2 days ago by
Kevin Blighe
87k
13
votes
13
replies
18k
views
9 follow
How Do I Translate Multiple (More Than 25000) Dna Sequences With Different Frames To Protein Seuquence?
dna
protein
updated 18 days ago by
ummeswaiba
• 0 • written 10.3 years ago by
biostar
▴ 170
1
vote
7
replies
15k
views
7 follow
How To Annotate Methylation 450K?
methylation
updated 22 days ago by
Vassilis
• 0 • written 10.1 years ago by
liu4gre
▴ 210
17
votes
16
replies
14k
views
10 follow
How to extract the longest isoform from multi fasta file
perl
extract
fasta
python
isoform
updated 23 days ago by
Madeleine
• 0 • written 9.8 years ago by
jon.brate
▴ 310
4
votes
4
replies
14k
views
Heatmap with custom gene labels annotated on the rows
differential-gene-expression
RNAseq
heatmap
updated 17 days ago by
Ram
43k • written 4.7 years ago by
bioinforesearchquestions
▴ 370
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 8 days ago by
colindaven
6.4k • written 10.9 years ago by
Ontheway
▴ 10
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 14 hours ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
37
votes
5
replies
13k
views
How do you generate TMM normalized counts using EdgeR?
R
RNA-seq
edgeR
updated 16 days ago by
inedraylig
▴ 60 • written 2.9 years ago by
Pratik
★ 1.0k
1
vote
4
replies
13k
views
RNA sequencing data batch effect removal
RNA-Seq
batch-effect
updated 8 days ago by
Ram
43k • written 7.4 years ago by
Tenghui Chen
• 0
17
votes
8
replies
12k
views
9 follow
MAF vs VAF
sequencing
updated 23 days ago by
AshleeThomson
▴ 80 • written 6.1 years ago by
lauren.wahyudi
▴ 50
10
votes
37
replies
12k
views
21 follow
Convert Gene IDs of Tomato Sol Database
tomato
gene
updated 16 days ago by
aziz.hammou
• 0 • written 8.8 years ago by
kevluv93
▴ 170
49
votes
30
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 29 days ago by
Istvan Albert
100k • written 8.2 years ago by
Ram
43k
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly
statistics
updated 13 days ago by
skdv2522
• 0 • written 4.7 years ago by
margab
▴ 10
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch-effect
updated 10 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
3
votes
6
replies
11k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker
Masking
updated 10 days ago by
Bioinfotec
▴ 10 • written 7.6 years ago by
nut_B
▴ 10
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 5 days ago by
Ram
43k • written 10.6 years ago by
Louis
▴ 150
4
votes
3
replies
10k
views
short and long reads
long-reads
Assembly
short-reads
updated 21 days ago by
Ram
43k • written 9.9 years ago by
midox
▴ 290
10
votes
6
replies
9.8k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 19 hours ago by
Antonio R. Franco
★ 5.1k • written 6.0 years ago by
williamsbrian5064
▴ 510
23
votes
23
replies
9.8k
views
6 follow
How to see if adjusting batch effect in RNA-seq is working or not
RNA-Seq
removeBatchEffect
batch-effect
edger
updated 9 days ago by
Ram
43k • written 5.3 years ago by
iraia.munoa
▴ 130
5
votes
13
replies
9.2k
views
8 follow
biomaRt: Timeout on getBM().
r
biomart
ensembl
updated 15 days ago by
Mike Smith
★ 2.0k • written 2.8 years ago by
lincaijin1994
▴ 40
3
votes
10
replies
8.5k
views
6 follow
GATK HaolotypeCaller takes too much time for variant calling
HaplotypeCaller
GATK
updated 21 days ago by
Ram
43k • written 6.4 years ago by
J.F.Jiang
▴ 920
3
votes
6
replies
8.4k
views
RNA-seq, EdgeR and batch effects
RNA-Seq
removeBatchEffect
edgeR
batch-effect
updated 10 days ago by
Ram
43k • written 9.3 years ago by
Ekarl2
▴ 120
4
votes
3
replies
7.6k
views
Genotype representation with 0, 1, 2 - what do they mean?
genotype
representation
phasing
imputation
gwas
updated 22 days ago by
far
• 0 • written 5.9 years ago by
Volka
▴ 180
4
votes
3
replies
7.4k
views
How to find/decipher Trimmomatic Output
trimmomatic
RNA-Seq
QC
updated 28 days ago by
Ram
43k • written 8.1 years ago by
nikelle.petrillo
▴ 110
5
votes
6
replies
7.3k
views
scatter plot, aov()
aov
scatter-plot
anova
updated 9 days ago by
Ram
43k • written 3.2 years ago by
Rob
▴ 170
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq
bulk-RNASeq
RNA-Seq
single-cell
updated 16 days ago by
veldahan86
• 0 • written 3.8 years ago by
Assa Yeroslaviz
★ 1.8k
10
votes
7
replies
7.1k
views
6 follow
Convert GVF to VCF
vcf
updated 10 days ago by
george-hall-ucl
• 0 • written 9.2 years ago by
win
▴ 970
14
votes
2
replies
7.0k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 2 days ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 1.4k
9
votes
3
replies
7.0k
views
EdgeR-GLMs correcting for batch effects
RNA-Seq
edgeR
Batch-Effect
updated 8 days ago by
Ram
43k • written 9.9 years ago by
Matina
▴ 250
11
votes
9
replies
6.9k
views
How to choose method to integrate different patient sample together in Seurat
Seurat
scRNA
batch-effect
harmony
updated 9 days ago by
Ram
43k • written 4.2 years ago by
623202215
▴ 80
9
votes
10
replies
6.9k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat
scRNA-seq
Harmony
RNA-seq
batch-effect
updated 8 days ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
6
votes
17
replies
6.6k
views
Can you add a label key to heatscatter plot in R?
heatscatter
visualization
R
updated 9 days ago by
Ram
43k • written 9.6 years ago by
james.lloyd
▴ 100
0
votes
4
replies
6.5k
views
fastq-dump: command not found, what is wrong?
assembly
sratoolkit
genomics
updated 24 days ago by
spalmer
• 0 • written 2.7 years ago by
BioinfoNoob6
• 0
7
votes
20
replies
6.4k
views
7 follow
Repeat masked gtf files from ensembl
ensembl
RNA-Seq
genome
updated 15 days ago by
e.r.zakiev
▴ 200 • written 4.3 years ago by
kevin.stachelek
▴ 80
13
votes
10
replies
6.4k
views
Adjusting for confounding variables in RNA-SEQ Differential Expression Analysis
Differential-Gene-Expression
RNA-Seq
Statistics
updated 17 days ago by
Ram
43k • written 5.7 years ago by
ucakhnd
▴ 40
3
votes
1
reply
6.2k
views
Normalization before or after merging the samples in Seurat
single-cell
seurat
batch-effect
updated 10 days ago by
Ram
43k • written 3.3 years ago by
fouerghi20
▴ 80
1
vote
3
replies
6.1k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID
org.Dr.eg.db
updated 10 days ago by
Ram
43k • written 5.5 years ago by
modarzi
▴ 170
22
votes
18
replies
6.1k
views
about batch correction in scRNA-seq
scRNA
scRNA-seq
batch-effect
updated 8 days ago by
Ram
43k • written 4.6 years ago by
Bogdan
★ 1.4k
12
votes
17
replies
6.1k
views
9 follow
ACMG assignment tools
wes
acmg
WES
WGS
updated 22 days ago by
Zuber
• 0 • written 3.9 years ago by
Eugene A
▴ 180
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 8 days ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
1,000 results • Page
1 of 20
Recent Votes
A: Blast Settings For Short Sequences
A: Blast Settings For Short Sequences
Comment: Heatmap and rna-seq
Answer: Heatmap and rna-seq
Comment: Heatmap and rna-seq
A: should FASTA files be sorted before indexed with SAMtools?
Answer: A faidx-indexed FASTA format file or a FASTA format file
Recent Locations •
All
India,
4 minutes ago
United States,
5 minutes ago
New York,
12 minutes ago
United States,
12 minutes ago
Chula Vista,
23 minutes ago
India,
28 minutes ago
United States,
38 minutes ago
Recent Awards •
All
Scholar
to
Alex Reynolds
35k
Popular Question
to
chaco001
▴ 40
Commentator
to
GenoMax
141k
Popular Question
to
rheab1230
▴ 140
Popular Question
to
BioinfGuru
★ 1.7k
Scholar
to
bk11
★ 2.4k
Popular Question
to
vinayjrao
▴ 250
Recent Replies
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
by
Gordon Smyth
★ 7.0k
There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler. I don't recommend col…
Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
by
Gordon Smyth
★ 7.0k
The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1. Have you exam…
Answer: How to use limma to find differentially expressed genes in response to a continu
by
Gordon Smyth
★ 7.0k
There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Thank you Pierre! I'll try this out with my full data set.
Answer: DNA methylation preprocessing
by
cao510927
▴ 30
I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Alex Reynolds
35k
I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
Comment: Highest variable features in single cell data
by
bk11
★ 2.4k
You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
Comment: Heatmap and rna-seq
by
GenoMax
141k
Please include a link when you are recommending a tool. There can be programs with similar names.
Answer: Heatmap and rna-seq
by
dsull
★ 5.8k
Check out clustergrammer from Avi Ma'ayan's lab.
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Ram
43k
Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
ATpoint
82k
You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 1.7k
Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
Comment: Low mapping rate with Salmon
by
i.sudbery
19k
Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.4k
If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value. https://www.b…
Traffic: 1606 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