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1,100 results • Page
2 of 22
Sort: Votes
Rank
Views
Votes
Replies
8
votes
6
replies
636
views
The bioinformatics paper reappears, but the results are significantly different from the original results
reproducibility
27 days ago by
jiao
▴ 40
8
votes
2
replies
793
views
News:
FINAL CALL - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (May 6-8, 2024 in Berlin)
single-cell
sequencing
26 days ago by
David Langenberger
11k
8
votes
16
replies
925
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 5 days ago by
bk11
★ 2.4k • written 8 weeks ago by
Sofia
• 0
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression
TPM
RNA-Seq
counts
batch-effect
14 days ago by
Ram
43k
8
votes
6
replies
2.5k
views
Batch effect removal with the help of sva
SVA
batch-effect
gene-expression
updated 23 days ago by
Ram
43k • written 3.5 years ago by
Gene_MMP8
▴ 240
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 29 days ago by
Maksim
• 0 • written 3.4 years ago by
progistar
▴ 40
8
votes
3
replies
372
views
How to extract rows with specific values in R for all the columns?
R
28 days ago by
Lakshmi
▴ 20
8
votes
5
replies
5.6k
views
ISCN annotation for SV/CN VCF files
SV
written 8 months ago by
a.beggs
▴ 60
8
votes
4
replies
3.0k
views
Read count correlation between samples
differential-gene-expression
RNA-seq
updated 22 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
8
votes
6
replies
2.6k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 14 days ago by
John Marshall
3.0k • written 24 months ago by
bioguy24
▴ 230
8
votes
5
replies
1.2k
views
Classifying repeat features from Ensembl
ensembl
repeat
updated 16 days ago by
e.r.zakiev
▴ 200 • written 16 months ago by
liorglic
★ 1.4k
8
votes
10
replies
742
views
bash script
whole-genome-sequencing
updated 16 days ago by
Ram
43k • written 23 days ago by
bestone
▴ 30
8
votes
8
replies
620
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 7 days ago by
swbarnes2
14k • written 8 days ago by
Aaliya
▴ 10
7
votes
6
replies
1.3k
views
using different microarray datasets (meta-analysis?) for DEG pipeline
microarray
meta-analysis
DEG
batch-effect
updated 14 days ago by
Ram
43k • written 4.9 years ago by
mosesoo
▴ 30
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 6 days ago by
rohitsatyam102
▴ 850 • written 6.1 years ago by
smallfish
▴ 10
7
votes
3
replies
4.6k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA
RNA-Seq
batch-effect
updated 14 days ago by
Ram
43k • written 5.1 years ago by
tujuchuanli
▴ 100
7
votes
3
replies
1.2k
views
biomaRt::getSequence - Invalid type argument
biomaRt
R
updated 15 days ago by
Ram
43k • written 3.9 years ago by
mbk0asis
▴ 680
7
votes
6
replies
517
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
10 days ago by
analyst
▴ 30
7
votes
8
replies
678
views
Why are the basics so complicated? Basic coverage filtering for VCF files
filter
vcf
coverage
updated 19 days ago by
spen
▴ 40 • written 22 days ago by
MBarcelo
▴ 40
7
votes
7
replies
1.1k
views
Prediction tools summary - zero values
statistics
updated 15 days ago by
Дана
• 0 • written 6 months ago by
Lukas
▴ 50
7
votes
7
replies
1.4k
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 16 days ago by
Dunois
★ 2.5k • written 17 days ago by
AdviceSeeker
• 0
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 15 days ago by
Ram
43k • written 2.0 years ago by
mmitra
▴ 60
7
votes
7
replies
582
views
Can you suggest a protein PDB that has two chainst but only 50 total number of atoms?
protein
pdb
protein-databank
updated 19 days ago by
Matthias Zepper
4.6k • written 19 days ago by
4fzcgueyp5
• 0
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 15 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
7
votes
2
replies
3.7k
views
Timeout on getBM() to retrieve snps from locations
biomaRt
getBM
R
updated 15 days ago by
Ram
43k • written 5.2 years ago by
Corentin
▴ 600
7
votes
2
replies
282
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 8 days ago by
geneontologyhelp
▴ 390 • written 9 days ago by
catherine.teyssier
• 0
7
votes
20
replies
6.4k
views
7 follow
Repeat masked gtf files from ensembl
ensembl
RNA-Seq
genome
updated 20 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 29 days ago by
Ram
43k • written 17 months ago by
Dunois
★ 2.5k
7
votes
4
replies
2.1k
views
filtering genes by pearson correlation
correlation
RNA-Seq
R
updated 15 days ago by
Ram
43k • written 6.1 years ago by
mannoulag1
▴ 120
7
votes
8
replies
687
views
6 follow
How to BLAST more than 5 sequences against UniProt database?
BLAST
Protein
UniProt
27 days ago by
Riq
▴ 50
7
votes
3
replies
2.9k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 13 days ago by
colindaven
6.4k • written 16 months ago by
Dr.Animo
▴ 130
6
votes
11
replies
3.3k
views
Collapsing probesets to genes on WGCNA
WGCNA
gene-expression
R
updated 15 days ago by
Ram
43k • written 5.3 years ago by
Davide Chicco
▴ 120
6
votes
4
replies
1.5k
views
RNA-Seq: X samples and X batches
RNA-Seq
edgeR
DESeq2
Batch-Effect
updated 15 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 15 days ago by
Ram
43k • written 9.6 years ago by
james.lloyd
▴ 100
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat
RNA-Seq
Limma
DESeq2
batch-effect
updated 13 days ago by
Ram
43k • written 5.0 years ago by
borkk
▴ 140
6
votes
4
replies
2.2k
views
Is there a way to get RNAFold output for multifasta in tabular format?
RNAFold
updated 14 days ago by
jakobjung
• 0 • written 4.6 years ago by
adhirajnath14
▴ 40
6
votes
2
replies
1.5k
views
Writing a batch script for analyzing RNA-Seq data
RNA-Seq
quantification
alignment
updated 15 days ago by
Ram
43k • written 5.2 years ago by
mohammedtoufiq91
▴ 250
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 13 days ago by
Ram
43k • written 7.0 years ago by
alexis.vandenbon
▴ 80
6
votes
3
replies
195
views
Interpretting IGV output
IGV
updated 10 days ago by
Carlo Yague
8.7k • written 10 days ago by
analyst
▴ 30
6
votes
10
replies
2.3k
views
Why different DEGs between my result and the author's result?
limma
microarray
differential-gene-expression
updated 22 days ago by
Ram
43k • written 6.1 years ago by
fernardo
▴ 170
6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna
RNA-Seq
ChIP-Seq
updated 23 days ago by
mflab
• 0 • written 3.9 years ago by
m.sadman.sakib
▴ 120
6
votes
3
replies
1.1k
views
How to normalize long-read RNA-seq data for comparison with short-reads
RNAseq
long-reads
normalization
short-reads
updated 29 days ago by
rpolicastro
13k • written 15 months ago by
Bernardo
▴ 30
6
votes
0
replies
200
views
Herald:
The Biostar Herald for Monday, April 15, 2024
herald
16 days ago by
Biostar
2.7k
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 14 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
6
votes
8
replies
589
views
BRAKER3 genome annotation
annotation
BRAKER3
genome
updated 14 days ago by
dariober
14k • written 17 days ago by
manaswiniparija3
▴ 40
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads
illumina
genome-assembly
updated 26 days ago by
Ram
43k • written 2.6 years ago by
predeus
★ 1.9k
6
votes
6
replies
4.4k
views
10x to cloupe
single-cell-transcriptomics
10x
22 days ago by
firestar
★ 1.6k
5
votes
20
replies
4.2k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression
RNA-seq
updated 22 days ago by
Ram
43k • written 6.2 years ago by
pablo61991
▴ 90
5
votes
3
replies
720
views
Illumina reads preprocessing best practice for snp calling applications
Illumina
snp
updated 12 days ago by
Enrique
• 0 • written 9 months ago by
Denis
▴ 310
5
votes
3
replies
243
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 2 days ago by
Lluís R.
★ 1.2k • written 2 days ago by
이민경[학생](대학원 융합의과학과)
• 0
1,100 results • Page
2 of 22
Recent Votes
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Answer: NGS forensics: how to know if data is fabricated
Comment: Adjust pvalue in R with different approach give me all different outcome
Comment: Bacterial plasmid analysis
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Comment: Odd alignment question/finding
by
ATpoint
82k
bwa mem is not fully deterministic, see from the developer: https://www.biostars.org/p/238628/#238817
Comment: How to perform single cell multimodal integration using Seurat for Geo datasets
by
ATpoint
82k
It's funny that you ask because the paper that these data were used for is called `Integrated analysis of multimodal single-cell data` from…
Comment: Odd alignment question/finding
by
liorglic
★ 1.4k
I can't come up with an explanation, but two things you can try for debugging are: 1) look at the fastp stats - do they add up and make sen…
Answer: Bacterial plasmid analysis
by
Mensur Dlakic
★ 27k
If you put all your sequences in separate files but in the same directory, this program will build a cladogram based on average nucleotide …
Comment: POSSUM not working due to incompatible pssm file
by
rianna.collins
• 0
Thank you so much. I'm new to this and didn't realise there was a code option.
Answer: Is there a way to increase the automatic label text size in Cytoscape?
by
Scooter
▴ 280
Greetings, Are you saying that you can't use the size setting in the style tab? That should certainly work, as should the label size se…
Answer: Basic stats in hierfstat
by
mdav
• 0
Hi Zoe, did you find an answer for this? I am also getting the same error.
Comment: GATK won't produce figures while analyzing covariates to generate 'recal_plots.p
by
GenoMax
141k
Your cluster may be missing libraries etc to create the PDF plots (this looks like a cluster job submission) on your cluster. Did you check…
Comment: Post-imputation plot
by
kl
▴ 10
Ok yes I think my thought was that given these errors, I could remove the mismatches and flip the alleles which seem to need flipping based…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
I think I will perhaps use their predominant PlasmidFinder type to group plasmids together and create separate core phylogenies for each as…
Comment: Bacterial plasmid analysis
by
GenoMax
141k
Can you classify the plasmids based on function (resistance genes they are carrying or some other criteria). Sizes above are indicating a w…
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by
ATpoint
82k
Initially posted here https://support.bioconductor.org/p/9158036/ where I suggested to put code and data and noted that GEOquery returns ar…
Answer: Post-imputation plot
by
LChart
3.9k
I agree that some need to be flipped (A/T and C/G where your panel frequency is 1 - ref panel frequency). There are other variants which yo…
Comment: RNA editing sites based on DNA seq and RNA seq
by
Adam
▴ 30
Are those 20% unaligned reads coming after hyper-editing detection?
Answer: How to find overlap of clusters in two seurat porject
by
Adam
▴ 30
I think your best bet would be to use annotation mapping. You can use the features of your clusters in group 1 and apply them to group 2 to…
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