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1,000 results • Page
2 of 20
Sort: Votes
Rank
Views
Votes
Replies
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 7 days ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
9
votes
4
replies
1.9k
views
Integration of RNA-Seq data with microarray data
microarray
RNA-Seq
batch-effect
R
updated 9 days ago by
Ram
43k • written 4.0 years ago by
Fahimeh.6868
▴ 30
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 24 days ago by
Ram
43k • written 16 months ago by
O.rka
▴ 710
9
votes
12
replies
4.1k
views
Batch effect, how to create a model matrix
RNA-Seq
deseq2
batch-effect
updated 8 days ago by
Ram
43k • written 4.9 years ago by
Mozart
▴ 330
8
votes
6
replies
2.6k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 8 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
8 days ago by
Ram
43k
8
votes
5
replies
1.2k
views
Classifying repeat features from Ensembl
ensembl
repeat
updated 11 days ago by
e.r.zakiev
▴ 200 • written 16 months ago by
liorglic
★ 1.4k
8
votes
3
replies
361
views
How to extract rows with specific values in R for all the columns?
R
22 days ago by
Lakshmi
▴ 20
8
votes
5
replies
5.1k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 60
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 23 days ago by
Maksim
• 0 • written 3.4 years ago by
progistar
▴ 40
8
votes
8
replies
523
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 1 day ago by
swbarnes2
14k • written 2 days ago by
Aaliya
▴ 10
8
votes
10
replies
698
views
bash script
whole-genome-sequencing
updated 10 days ago by
Ram
43k • written 18 days ago by
bestone
▴ 30
8
votes
16
replies
746
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 4 minutes ago by
bk11
★ 2.4k • written 7 weeks ago by
Sofia
• 0
8
votes
6
replies
2.5k
views
Batch effect removal with the help of sva
SVA
batch-effect
gene-expression
updated 17 days ago by
Ram
43k • written 3.5 years ago by
Gene_MMP8
▴ 240
8
votes
6
replies
616
views
The bioinformatics paper reappears, but the results are significantly different from the original results
reproducibility
21 days ago by
jiao
▴ 40
8
votes
4
replies
3.0k
views
Read count correlation between samples
differential-gene-expression
RNA-seq
updated 16 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
8
votes
2
replies
777
views
News:
FINAL CALL - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (May 6-8, 2024 in Berlin)
single-cell
sequencing
21 days ago by
David Langenberger
11k
7
votes
2
replies
3.7k
views
Timeout on getBM() to retrieve snps from locations
biomaRt
getBM
R
updated 9 days ago by
Ram
43k • written 5.2 years ago by
Corentin
▴ 600
7
votes
8
replies
653
views
Why are the basics so complicated? Basic coverage filtering for VCF files
filter
vcf
coverage
updated 13 days ago by
spen
▴ 40 • written 17 days ago by
MBarcelo
▴ 40
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 23 hours ago by
rohitsatyam102
▴ 850 • written 6.1 years ago by
smallfish
▴ 10
7
votes
7
replies
1.0k
views
Prediction tools summary - zero values
statistics
updated 9 days ago by
Дана
• 0 • written 6 months ago by
Lukas
▴ 50
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
7
votes
3
replies
2.8k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 7 days ago by
colindaven
6.4k • written 15 months ago by
Dr.Animo
▴ 130
7
votes
6
replies
466
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
5 days ago by
analyst
▴ 30
7
votes
7
replies
1.2k
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 10 days ago by
Dunois
★ 2.5k • written 11 days ago by
AdviceSeeker
• 0
7
votes
8
replies
667
views
6 follow
How to BLAST more than 5 sequences against UniProt database?
BLAST
Protein
UniProt
21 days ago by
Riq
▴ 50
7
votes
4
replies
2.1k
views
filtering genes by pearson correlation
correlation
RNA-Seq
R
updated 9 days ago by
Ram
43k • written 6.1 years ago by
mannoulag1
▴ 120
7
votes
3
replies
4.6k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA
RNA-Seq
batch-effect
updated 8 days ago by
Ram
43k • written 5.1 years ago by
tujuchuanli
▴ 100
7
votes
6
replies
1.3k
views
using different microarray datasets (meta-analysis?) for DEG pipeline
microarray
meta-analysis
DEG
batch-effect
updated 8 days ago by
Ram
43k • written 4.9 years ago by
mosesoo
▴ 30
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 9 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 9 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
7
votes
7
replies
550
views
Can you suggest a protein PDB that has two chainst but only 50 total number of atoms?
protein
pdb
protein-databank
updated 13 days ago by
Matthias Zepper
4.5k • written 14 days ago by
4fzcgueyp5
• 0
7
votes
2
replies
262
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 2 days ago by
geneontologyhelp
▴ 390 • written 3 days ago by
catherine.teyssier
• 0
7
votes
3
replies
1.2k
views
biomaRt::getSequence - Invalid type argument
biomaRt
R
updated 9 days ago by
Ram
43k • written 3.8 years ago by
mbk0asis
▴ 680
7
votes
4
replies
1.9k
views
AlphaFold 2 alternatives
protein-structure
alphafold
updated 24 days ago by
Ram
43k • written 17 months ago by
Dunois
★ 2.5k
6
votes
4
replies
2.2k
views
Is there a way to get RNAFold output for multifasta in tabular format?
RNAFold
updated 9 days ago by
jakobjung
• 0 • written 4.6 years ago by
adhirajnath14
▴ 40
6
votes
13
replies
608
views
Variant calling of GBS data
GBS
variants
BQSR
28 days ago by
analyst
▴ 30
6
votes
4
replies
1.5k
views
RNA-Seq: X samples and X batches
RNA-Seq
edgeR
DESeq2
Batch-Effect
updated 9 days ago by
Ram
43k • written 5.2 years ago by
Behram Radmanesh
▴ 40
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
6
votes
0
replies
190
views
Herald:
The Biostar Herald for Monday, April 15, 2024
herald
11 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 20 days ago by
Ram
43k • written 2.6 years ago by
predeus
★ 1.9k
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 7 days ago by
Ram
43k • written 7.0 years ago by
alexis.vandenbon
▴ 80
6
votes
10
replies
2.3k
views
Why different DEGs between my result and the author's result?
limma
microarray
differential-gene-expression
updated 16 days ago by
Ram
43k • written 6.1 years ago by
fernardo
▴ 170
6
votes
8
replies
544
views
BRAKER3 genome annotation
annotation
BRAKER3
genome
updated 9 days ago by
dariober
14k • written 11 days ago by
manaswiniparija3
▴ 40
6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna
RNA-Seq
ChIP-Seq
updated 18 days ago by
mflab
• 0 • written 3.9 years ago by
m.sadman.sakib
▴ 120
6
votes
6
replies
4.3k
views
10x to cloupe
single-cell-transcriptomics
10x
17 days ago by
firestar
★ 1.6k
6
votes
2
replies
1.5k
views
Writing a batch script for analyzing RNA-Seq data
RNA-Seq
quantification
alignment
updated 9 days ago by
Ram
43k • written 5.1 years ago by
mohammedtoufiq91
▴ 250
6
votes
11
replies
3.3k
views
Collapsing probesets to genes on WGCNA
WGCNA
gene-expression
R
updated 9 days ago by
Ram
43k • written 5.2 years ago by
Davide Chicco
▴ 120
6
votes
3
replies
179
views
Interpretting IGV output
IGV
updated 4 days ago by
Carlo Yague
8.7k • written 4 days ago by
analyst
▴ 30
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 8 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
1,000 results • Page
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Recent Votes
A: How to process (seems) Agilent microarrry data?
Comment: genome assembly records not present in assembly_summary.txt
Answer: genome assembly records not present in assembly_summary.txt
Answer: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
Comment: PCA plot (Suggestions Needed)
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Recent Replies
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…
Comment: genome assembly records not present in assembly_summary.txt
by
sapuizait
▴ 10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question
by
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★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Comment: Low mapping rate with Salmon
by
GenoMax
141k
> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes? Reads are likely aligning in regions wh…
Comment: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
cmdcolin
★ 3.8k
the gencode link is broken now but here is a back up of that blogpost on archive https://web.archive.org/web/20130618221342/http://gencodeg…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
I'll try to make the decoy file again but I remember you also told me that it is only recommended and not mandatory for running `salmon`. I…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
For doing this, should I just look at the log.out.file?
Answer: Heatmap and rna-seq
by
pinheirofabiano
▴ 10
install.packages("pheatmap") library(pheatmap) setwd("/Users/data_analysis/results") data <- read.table(file…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
Thanks for the link GenoMax. But I was wondering, should not alignment and mapping have a similar rate and thus be correlated? In my case I…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
bedtools intersect \ -a <(sort -t $'\t' -k1,1 -k2,2n A.bed) \ -b <(awk '{X=250000;P=int($2);printf("%s\t…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
Comment: ScRNA data question
by
starswillfade
▴ 10
I just thought it was weird that considering each dot is a cell their expressions were all on a single line instead of being spread out lik…
Comment: ScRNA data question
by
starswillfade
▴ 10
![enter image description here][1] I am already using Seurat V5 I think. I am using SCTransform as it was recommended by the seurat page. I…
Answer: genome assembly records not present in assembly_summary.txt
by
GenoMax
141k
Can you clarify what `metainfo` you are referring to? The accession that you refer to does exist in [**GenBank assembly_summary file**][1…
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