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
1,154 results • Page
2 of 24
Sort: Votes
Rank
Views
Votes
Replies
9
votes
6
replies
1.5k
views
What in silico PCR commandline tool do you use that can handle IUPAC characters?
pcr
amplicon
primer
updated 22 days ago by
Ram
43k • written 16 months ago by
O.rka
▴ 710
9
votes
5
replies
2.2k
views
Millions of Reads Needed for Differential Gene Expression
differential-gene-expression
RNA-Seq
deseq2
updated 15 days ago by
Ram
43k • written 4.6 years ago by
contact
▴ 20
9
votes
3
replies
6.9k
views
EdgeR-GLMs correcting for batch effects
RNA-Seq
edgeR
Batch-Effect
updated 6 days ago by
Ram
43k • written 9.9 years ago by
Matina
▴ 250
9
votes
4
replies
1.9k
views
Integration of RNA-Seq data with microarray data
microarray
RNA-Seq
batch-effect
R
updated 8 days ago by
Ram
43k • written 4.0 years ago by
Fahimeh.6868
▴ 30
9
votes
12
replies
4.1k
views
Batch effect, how to create a model matrix
RNA-Seq
deseq2
batch-effect
updated 7 days ago by
Ram
43k • written 4.9 years ago by
Mozart
▴ 330
8
votes
6
replies
2.5k
views
Batch effect removal with the help of sva
SVA
batch-effect
gene-expression
updated 16 days ago by
Ram
43k • written 3.5 years ago by
Gene_MMP8
▴ 240
8
votes
10
replies
692
views
bash script
whole-genome-sequencing
updated 9 days ago by
Ram
43k • written 16 days ago by
bestone
▴ 30
8
votes
3
replies
357
views
How to extract rows with specific values in R for all the columns?
R
21 days ago by
Lakshmi
▴ 20
8
votes
5
replies
4.9k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 60
8
votes
4
replies
3.0k
views
Read count correlation between samples
differential-gene-expression
RNA-seq
updated 15 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
8
votes
5
replies
1.2k
views
Classifying repeat features from Ensembl
ensembl
repeat
updated 9 days ago by
e.r.zakiev
▴ 200 • written 16 months ago by
liorglic
★ 1.4k
8
votes
6
replies
2.6k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 7 days ago by
John Marshall
3.0k • written 24 months ago by
bioguy24
▴ 230
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression
TPM
RNA-Seq
counts
batch-effect
7 days ago by
Ram
43k
8
votes
6
replies
609
views
The bioinformatics paper reappears, but the results are significantly different from the original results
reproducibility
19 days ago by
jiao
▴ 40
8
votes
2
replies
766
views
News:
FINAL CALL - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (May 6-8, 2024 in Berlin)
single-cell
sequencing
19 days ago by
David Langenberger
11k
8
votes
12
replies
3.5k
views
Why should ATAC-seq mapped reads be shifted +4 and -5 for +strand and -strand, respectively
ATAC-seq
updated 21 days ago by
Maksim
• 0 • written 3.4 years ago by
progistar
▴ 40
7
votes
10
replies
2.7k
views
6 follow
Batch effect correction to compare differentially expressed genes across datasets
batch
batch-effect
DESeq2
rna-seq
updated 8 days ago by
Ram
43k • written 2.0 years ago by
mmitra
▴ 60
7
votes
4
replies
1.4k
views
Is there any journal article to reference removeBatchEffect function from Limma?
batch
removebatcheffect
limma
rna-seq
batch-effect
updated 8 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
7
votes
4
replies
2.1k
views
filtering genes by pearson correlation
correlation
RNA-Seq
R
updated 7 days ago by
Ram
43k • written 6.1 years ago by
mannoulag1
▴ 120
7
votes
3
replies
1.2k
views
biomaRt::getSequence - Invalid type argument
biomaRt
R
updated 7 days ago by
Ram
43k • written 3.8 years ago by
mbk0asis
▴ 680
7
votes
7
replies
1.1k
views
Forum:
Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career
advice
updated 9 days ago by
Dunois
★ 2.5k • written 10 days ago by
AdviceSeeker
• 0
7
votes
8
replies
648
views
Why are the basics so complicated? Basic coverage filtering for VCF files
filter
vcf
coverage
updated 12 days ago by
spen
▴ 40 • written 15 days ago by
MBarcelo
▴ 40
7
votes
6
replies
447
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
3 days ago by
analyst
▴ 30
7
votes
3
replies
4.5k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA
RNA-Seq
batch-effect
updated 7 days ago by
Ram
43k • written 5.1 years ago by
tujuchuanli
▴ 100
7
votes
2
replies
3.6k
views
Timeout on getBM() to retrieve snps from locations
biomaRt
getBM
R
updated 7 days ago by
Ram
43k • written 5.2 years ago by
Corentin
▴ 600
7
votes
8
replies
660
views
6 follow
How to BLAST more than 5 sequences against UniProt database?
BLAST
Protein
UniProt
20 days ago by
Riq
▴ 50
7
votes
3
replies
2.8k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 5 days ago by
colindaven
6.4k • written 15 months ago by
Dr.Animo
▴ 130
7
votes
2
replies
220
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 1 day ago by
geneontologyhelp
▴ 390 • written 2 days ago by
catherine.teyssier
• 0
7
votes
7
replies
543
views
Can you suggest a protein PDB that has two chainst but only 50 total number of atoms?
protein
pdb
protein-databank
updated 12 days ago by
Matthias Zepper
4.5k • written 12 days ago by
4fzcgueyp5
• 0
7
votes
7
replies
1.0k
views
Prediction tools summary - zero values
statistics
updated 8 days ago by
Дана
• 0 • written 6 months ago by
Lukas
▴ 50
7
votes
2
replies
251
views
Create a new reference genome with denovo assembly and standard reference with long read data?
PacBio
updated 29 days ago by
gconcepcion
▴ 410 • written 29 days ago by
eorr
▴ 30
7
votes
20
replies
6.4k
views
7 follow
Repeat masked gtf files from ensembl
ensembl
RNA-Seq
genome
updated 13 days ago by
e.r.zakiev
▴ 200 • written 4.3 years ago by
kevin.stachelek
▴ 80
7
votes
4
replies
1.9k
views
AlphaFold 2 alternatives
protein-structure
alphafold
updated 22 days ago by
Ram
43k • written 17 months ago by
Dunois
★ 2.5k
7
votes
6
replies
1.3k
views
using different microarray datasets (meta-analysis?) for DEG pipeline
microarray
meta-analysis
DEG
batch-effect
updated 7 days ago by
Ram
43k • written 4.8 years ago by
mosesoo
▴ 30
6
votes
11
replies
3.3k
views
Collapsing probesets to genes on WGCNA
WGCNA
gene-expression
R
updated 7 days ago by
Ram
43k • written 5.2 years ago by
Davide Chicco
▴ 120
6
votes
2
replies
1.5k
views
Writing a batch script for analyzing RNA-Seq data
RNA-Seq
quantification
alignment
updated 8 days ago by
Ram
43k • written 5.1 years ago by
mohammedtoufiq91
▴ 250
6
votes
3
replies
161
views
Interpretting IGV output
IGV
updated 2 days ago by
Carlo Yague
8.7k • written 2 days ago by
analyst
▴ 30
6
votes
0
replies
189
views
Herald:
The Biostar Herald for Monday, April 15, 2024
herald
9 days ago by
Biostar
2.7k
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads
illumina
genome-assembly
updated 19 days ago by
Ram
43k • written 2.6 years ago by
predeus
★ 1.9k
6
votes
6
replies
4.3k
views
10x to cloupe
single-cell-transcriptomics
10x
15 days ago by
firestar
★ 1.6k
6
votes
4
replies
1.5k
views
RNA-Seq: X samples and X batches
RNA-Seq
edgeR
DESeq2
Batch-Effect
updated 7 days ago by
Ram
43k • written 5.2 years ago by
Behram Radmanesh
▴ 40
6
votes
0
replies
2.6k
views
Tool:
Immuno-Navigator, a batch-corrected database for gene coexpression in the immune system
gene-co-expression
batch-effect
immunology
updated 6 days ago by
Ram
43k • written 7.0 years ago by
alexis.vandenbon
▴ 80
6
votes
13
replies
595
views
Variant calling of GBS data
GBS
variants
BQSR
27 days ago by
analyst
▴ 30
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat
RNA-Seq
Limma
DESeq2
batch-effect
updated 6 days ago by
Ram
43k • written 4.9 years ago by
borkk
▴ 140
6
votes
9
replies
1.8k
views
How to convert .wib files to .wig or .bed?
wib
BED
wig
bedtools
28 days ago by
Zeng Jingyu
▴ 60
6
votes
8
replies
538
views
BRAKER3 genome annotation
annotation
BRAKER3
genome
updated 7 days ago by
dariober
14k • written 9 days ago by
manaswiniparija3
▴ 40
6
votes
12
replies
5.7k
views
6 follow
Getting sample information from GEO
GEO
NCBI
updated 29 days ago by
Tania
• 0 • written 6.9 years ago by
Tom_L
▴ 350
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 7 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna
RNA-Seq
ChIP-Seq
updated 16 days ago by
mflab
• 0 • written 3.9 years ago by
m.sadman.sakib
▴ 120
6
votes
17
replies
6.6k
views
Can you add a label key to heatscatter plot in R?
heatscatter
visualization
R
updated 7 days ago by
Ram
43k • written 9.5 years ago by
james.lloyd
▴ 100
1,154 results • Page
2 of 24
Recent Votes
Answer: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
Recent Locations •
All
United States,
just now
United States,
6 minutes ago
United States,
7 minutes ago
South Korea,
7 minutes ago
China,
9 minutes ago
United States,
13 minutes ago
Russia,
16 minutes ago
Recent Awards •
All
Popular Question
to
Simone
▴ 10
Popular Question
to
carlopecoraro2
★ 2.5k
Popular Question
to
daffodil
▴ 10
Popular Question
to
Russ
▴ 500
Popular Question
to
camillab.
▴ 160
Popular Question
to
pramach1
▴ 40
Popular Question
to
Adyasha
• 0
Recent Replies
Comment: clustalo - align milions of short seq, memory issue
by
emmanouil.a
▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
Comment: Annovar using R package
by
Pierre Lindenbaum
161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
Comment: Trouble with Pilon installation
by
Lissa Cruz Saavedra
• 0
Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
Comment: Adding CB tag to bam file
by
swbarnes2
14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model
by
biochugs
• 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
DKA
▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed)
by
Mensur Dlakic
★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model
by
Mensur Dlakic
★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least one additional problem on top of …
Answer: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file
by
GenoMax
141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
GenoMax
141k
Please post information about your tool as a `tools` category post. Don't wait/ask other users to ask you.
Comment: Adding CB tag to bam file
by
Maria
• 0
Sorry for the delay in my answer, I got sidetracked. I am using ```samtools addreplacerg -r "@RG\tID:$cell" -o $cell.bam -h $LINE``` bu…
Answer: Troubleshooting RNA-seq data with DNA contamination
by
haibol2017
▴ 10
We just developed a R package to tackle this problem. Do you have stranded or unstranded RNA-seq data contaminated with gDNA? If you wou…
Traffic: 1954 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