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
960 results • Page
4 of 20
Sort: Votes
Rank
Views
Votes
Replies
4
votes
5
replies
1.9k
views
which package should be selected for differential gene expression analysis
Differential-gene-expression
RNA-Seq
updated 26 days ago by
Ram
43k • written 5.5 years ago by
lkianmehr
▴ 100
4
votes
6
replies
500
views
Odd results with BLAST remote
blast
remote
NCBI
updated 19 days ago by
b.contreras.moreira
▴ 180 • written 20 days ago by
Begonia_pavonina
▴ 150
4
votes
4
replies
14k
views
Heatmap with custom gene labels annotated on the rows
differential-gene-expression
RNAseq
heatmap
updated 26 days ago by
Ram
43k • written 4.7 years ago by
bioinforesearchquestions
▴ 370
4
votes
4
replies
392
views
Bowtie2 mapping is slow
metagenomics
bowtie2
mapping
read
updated 23 days ago by
colindaven
6.4k • written 4 weeks ago by
Md Moinuddin
• 0
3
votes
2
replies
822
views
Retrieve initial query in getBM()
getBM
biomaRt
R
gene
updated 18 days ago by
Ram
43k • written 3.2 years ago by
helia.ziaei
• 0
3
votes
6
replies
4.0k
views
Loading previously downloaded GEO SOfT data into R, using getGEO from GEOquery package
microarray
r
GEOquery
updated 18 days ago by
Ram
43k • written 5.0 years ago by
mosesoo
▴ 30
3
votes
5
replies
1.4k
views
Removing Batch effect that is the same as condition - DESEq2
RNA-Seq
batch-effect
DESeq2
updated 27 days ago by
Ram
43k • written 3.9 years ago by
annamariabugaj
• 0
3
votes
7
replies
519
views
Integration of transcriptomics and proteomics: difficult matching names
rna-seq
tmt
nomenclature
proteomics
19 days ago by
ntsopoul
▴ 60
3
votes
2
replies
379
views
Extract protein sequence
fasta
alignment
blast
5 days ago by
anna
▴ 20
3
votes
3
replies
736
views
KissDE and batch effect
kissDE
kissplice
13 days ago by
david.b.rombaut
▴ 10
3
votes
1
reply
459
views
Can anyone give me the code for in-silico digestion of whole genome with two restriction enzyme in "R" through Biostrings package?
whole-genome
In-silico-digestion
updated 27 days ago by
Ram
43k • written 29 days ago by
Bhowmik
▴ 10
3
votes
16
replies
2.7k
views
design matrix for dge
limma
differential-gene-expression
r
updated 26 days ago by
Ram
43k • written 7.9 years ago by
1234anjalianjali1234
▴ 50
3
votes
5
replies
315
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 13 days ago by
GenoMax
142k • written 13 days ago by
ahmad.sajad4541
• 0
3
votes
11
replies
6.0k
views
Modifying R pairs() function
plotMEpairs
WGCNA
R
updated 18 days ago by
Ram
43k • written 6.4 years ago by
shania90.lk
▴ 30
3
votes
4
replies
3.5k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 17 days ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
3
votes
4
replies
3.8k
views
Error in ComBat function: Error in dat[, batch == batch_level] : (subscript) logical subscript too long
Batch-effect
microarray
R
updated 18 days ago by
Ram
43k • written 2.9 years ago by
Sib
▴ 60
3
votes
9
replies
523
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 11 days ago by
Istvan Albert
100k • written 13 days ago by
Κοσμάς
• 0
3
votes
3
replies
323
views
Bwa sampe - BGI
Bwa-sampe
BGI
updated 19 days ago by
GenoMax
142k • written 19 days ago by
lorena9132
▴ 10
3
votes
3
replies
315
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 9 days ago by
GenoMax
142k • written 9 days ago by
sapuizait
▴ 10
3
votes
5
replies
1.3k
views
How to identify antibiotic resistant genes in gene databases?
antibiotic
Gene-Ontology
GO
updated 24 days ago by
Ram
43k • written 2.1 years ago by
ramin.k2013
• 0
3
votes
3
replies
2.4k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 10 days ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
3
votes
2
replies
1.0k
views
Can I take 'organ type' as a batch effect and use ComBat to remove organ dependent variations?
RNA-Seq
Cross-Species
SVA
ComBat
Batch-Effect
updated 18 days ago by
Ram
43k • written 4.7 years ago by
rodguinea
• 0
3
votes
6
replies
901
views
Any problem re-using last year's RNA-Seq data in this year's analysis?
RNA-Seq
batch-effect
updated 18 days ago by
Ram
43k • written 3.7 years ago by
oakhamwolf
▴ 20
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 days ago by
Ram
43k • written 4.6 years ago by
hkarakurt
▴ 180
3
votes
3
replies
560
views
Korean human genome reference file
GWAS
reference
imputation
16 days ago by
SeoGyun
• 0
3
votes
2
replies
4.2k
views
Batch effects in sequencing data
batch-effect
updated 17 days ago by
Ram
43k • written 8.7 years ago by
Andrew
▴ 60
3
votes
4
replies
402
views
How to download large-scale cDNA sequences from NCBI effectively ?
NCBI.
cDNA
updated 22 days ago by
Pierre Lindenbaum
161k • written 22 days ago by
Sony
▴ 10
3
votes
5
replies
243
views
Generating mpileup file using samtools
mpileup
samtools
updated 2 days ago by
Joe
21k • written 2 days ago by
Ruqaiya
• 0
3
votes
4
replies
715
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
13 days ago by
rahu
• 0
3
votes
3
replies
344
views
Visualize pathways from MSigDB
MSigdb
29 days ago by
Chris
▴ 260
3
votes
3
replies
334
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 9 days ago by
swbarnes2
14k • written 10 days ago by
M
• 0
3
votes
1
reply
278
views
how to change the gene header names in a fasta file?
fasta
bioawk
awk
seqkit
updated 23 days ago by
Ram
43k • written 24 days ago by
rj.rezwan
• 0
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 3 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
3
votes
0
replies
137
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 12 days ago by
Ram
43k • written 12 days ago by
carlopecoraro2
★ 2.5k
3
votes
5
replies
607
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
13 days ago by
n_navy
• 0
3
votes
5
replies
301
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
2 days ago by
Maverick
▴ 10
3
votes
3
replies
642
views
Why are there several gene expression files (for example, miRNA) in TCGA for one case?
Differential-gene-expression
TCGA
miRNA
updated 26 days ago by
Ram
43k • written 5 months ago by
mohammadhassanj
▴ 260
3
votes
3
replies
517
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 15 days ago by
swbarnes2
14k • written 16 days ago by
noodle
▴ 580
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 8 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
3
votes
2
replies
2.1k
views
Batch effect correction - miRNA sequencing - DESeq2
Batch-effect
DESeq2
miRNA-Seq
updated 18 days ago by
Ram
43k • written 5.5 years ago by
prekrish
• 0
3
votes
1
reply
618
views
What is the normalization status of metabric data?
metabric
normalization
microarray
cbioportal
updated 17 days ago by
etiennedanis
▴ 20 • written 19 months ago by
DareDevil
★ 4.3k
3
votes
0
replies
169
views
Herald:
The Biostar Herald for Tuesday, April 09, 2024
herald
26 days ago by
Biostar
2.7k
3
votes
2
replies
5.2k
views
RNASeq: Differential gene expression and qqplot
limma
differential-gene-expression
RNA-Seq
deseq2
updated 26 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
3
votes
4
replies
3.3k
views
Motif analysis of DMRs (Differentially Methylated Regions) by HOMER
next-gen
updated 24 days ago by
Ram
43k • written 6.7 years ago by
inschigu
▴ 10
3
votes
3
replies
3.0k
views
Quick way to Identify batch effect from covariates?
bioconductor
batch-effect
updated 17 days ago by
Ram
43k • written 7.9 years ago by
James Ashmore
★ 3.4k
3
votes
0
replies
1.1k
views
Tool:
Sars-Cov-2 Genome & ACE 2 Exploration
sequence
alignment
SNP
genome
11 hours ago by
Ibrahim Tanyalcin
★ 1.2k
3
votes
10
replies
666
views
Piping samtools to R
R
NGS
bash
samtools
18 days ago by
noodle
▴ 580
3
votes
3
replies
357
views
Disrupting a gene interaction network
cytohubba
cytoscape
sequences
mRNA
24 days ago by
george
• 0
3
votes
7
replies
1.0k
views
Can I use batch effect correction "by parts"?
ComBat
RNA-Seq
batch-effect
updated 18 days ago by
Ram
43k • written 4.3 years ago by
n,n
▴ 360
3
votes
1
reply
284
views
ClueGO is not showing custom data
ClueGo
Cytoscape
updated 24 days ago by
Scooter
▴ 280 • written 4 weeks ago by
Nicolas
• 0
960 results • Page
4 of 20
Recent Votes
A: Fold change - a final explanation
Answer: sc/snRNASeq using cell ranger parameters
mitochondria in single nuclear RNAseq
Answer: Association study using SNP data
Comment: agilent human all exon sureselct v7 bed file
Answer: install package
Comment: Overlap File for RACON Genome Polisher
Recent Locations •
All
United States,
just now
France/Nantes/Institut du Thorax - INSERM UMR1087,
just now
Whitefish, MT,
2 minutes ago
Turkey,
3 minutes ago
Italy,
6 minutes ago
United States,
8 minutes ago
Mexico,
11 minutes ago
Recent Awards •
All
Commentator
to
andres.firrincieli
3.6k
Popular Question
to
qudrat.nii
▴ 10
Popular Question
to
arctic
▴ 40
Popular Question
to
iamsmor
• 0
Popular Question
to
carlopecoraro2
★ 2.5k
Popular Question
to
Sara
▴ 30
Popular Question
to
Assa Yeroslaviz
★ 1.8k
Recent Replies
Comment: Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so t
by
mropri
▴ 150
Hi, I just wanted to update that IEGscore and PCNAscore were linearly dependent (or linear combinations of each other). I tested this using…
Comment: TaxID mapping file
by
Lada
▴ 30
if I understood correctly, I might need fle `prot.accession2taxid.gz` file? According to the [documentation][1] in column 2 is Accession.ve…
Answer: install package
by
Pine
▴ 10
To follow on Mathew's reply, one way might be to try and see if you can download and install the package tarball locally: 1. Get the packag…
Comment: agilent human all exon sureselct v7 bed file
by
MiladAD
▴ 10
God bless you man.
Answer: install package
by
Mathew
▴ 50
Hi, This is what happens when I run some code to diagnose the issue. First, I wanted to see what version of R was required for the package…
Comment: TaxID mapping file
by
Lada
▴ 30
thank you, I'll look at these files/documents. .
Answer: LD-prune variants while maintaining a list of SNPs
by
Jautis
▴ 540
I was given a solution by a colleague -- it seems a little hacky, but worked really well! > one way to get this to work is to use --clu…
Answer: Association study using SNP data
by
drajangirija
• 0
Hi Matthew, Thank you very much for your inputs. I am working with Neogen genotyping data, which includes GC values less than 0.15.
Comment: Downloading full alignments from Pfam
by
bef1
• 0
I tried contacting Pfam, they replied that indeed there is an issue on their side with the full alignments, which should be repaired in the…
Comment: Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Expe
by
Mensur Dlakic
★ 27k
Don't know about others, but I would never contact someone about potential employment based only on their interests and with zero knowledge…
Comment: The GDC Legacy Archive is retiring soon.
by
Zhenyu Zhang
★ 1.2k
If you are talking about methylation idat files, they were all migrated from legacy to the data portal. If you are talking about other pl…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Zhenyu Zhang
★ 1.2k
These TCGA samples were taken 10 ~ 20 years ago, and there is no way they have been treated by the modern immunotherapy. Are you sure tha…
Comment: Design matrix Differential expression analysis
by
Gordon Smyth
★ 7.1k
> When is it recommended to use the design <- cbind(Intercept=1,Group=c(-1,-1,-1,1,1,1)) It is not recommended. No such code appears anywh…
Comment: GRCh38.gmap file
by
lorena9132
▴ 10
Hi Mathew, The .txt files provided in the link differ from the .gmap files, but after several attempts, I succeeded in generating the .gma…
Answer: GRCh38.gmap file
by
Mathew
▴ 50
Hi, I have spent some time searching for a GRCH38 map file for you. I have found a certain publication that uses a hg38 genetic map file…
Traffic: 1595 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