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1,101 results • Page 2 of 23
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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
8
replies
621
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 7 days ago by 14k • written 8 days ago by ▴ 10
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
926
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 5 days ago by ★ 2.4k • written 8 weeks ago by • 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
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 • 0 • written 3.4 years ago by ▴ 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
6
replies
2.5k
views
Batch effect removal with the help of sva
SVA batch-effect gene-expression
updated 23 days ago by 43k • written 3.5 years ago by ▴ 240
8
votes
10
replies
742
views
bash script
whole-genome-sequencing
updated 16 days ago by 43k • written 24 days ago by ▴ 30
8
votes
4
replies
3.0k
views
Read count correlation between samples
differential-gene-expression RNA-seq
updated 22 days ago by 43k • written 6.5 years ago by ★ 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 3.0k • written 24 months ago by ▴ 230
8
votes
5
replies
1.2k
views
Classifying repeat features from Ensembl
ensembl repeat
updated 16 days ago by ▴ 200 • written 16 months ago by ★ 1.4k
8
votes
5
replies
5.6k
views
ISCN annotation for SV/CN VCF files
SV
written 8 months ago by ▴ 60
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 43k • written 5.1 years ago by ▴ 100
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 43k • written 4.9 years ago by ▴ 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 ▴ 850 • written 6.1 years ago by ▴ 10
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
3
replies
1.2k
views
biomaRt::getSequence - Invalid type argument
biomaRt R
updated 15 days ago by 43k • written 3.9 years ago by ▴ 680
7
votes
4
replies
2.1k
views
filtering genes by pearson correlation
correlation RNA-Seq R
updated 15 days ago by 43k • written 6.1 years ago by ▴ 120
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 ▴ 40 • written 22 days ago by ▴ 40
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 ★ 2.5k • written 17 days ago by • 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 43k • written 21 months ago by ▴ 20
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 43k • written 2.0 years ago by ▴ 60
7
votes
8
replies
688
views
6 follow
How to BLAST more than 5 sequences against UniProt database?
BLAST Protein UniProt
27 days ago by Riq ▴ 50
7
votes
20
replies
6.4k
views
7 follow
Repeat masked gtf files from ensembl
ensembl RNA-Seq genome
updated 20 days ago by ▴ 200 • written 4.3 years ago by ▴ 80
7
votes
7
replies
1.1k
views
Prediction tools summary - zero values
statistics
updated 15 days ago by • 0 • written 6 months ago by ▴ 50
7
votes
2
replies
3.7k
views
Timeout on getBM() to retrieve snps from locations
biomaRt getBM R
updated 15 days ago by 43k • written 5.2 years ago by ▴ 600
7
votes
2
replies
282
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 8 days ago by ▴ 390 • written 9 days ago by • 0
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 6.4k • written 16 months ago by ▴ 130
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 4.6k • written 19 days ago by • 0
7
votes
4
replies
1.9k
views
AlphaFold 2 alternatives
protein-structure alphafold
updated 29 days ago by 43k • written 17 months ago by ★ 2.5k
6
votes
11
replies
3.3k
views
Collapsing probesets to genes on WGCNA
WGCNA gene-expression R
updated 15 days ago by 43k • written 5.3 years ago by ▴ 120
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 43k • written 5.0 years ago by ▴ 140
6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna RNA-Seq ChIP-Seq
updated 23 days ago by • 0 • written 3.9 years ago by ▴ 120
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 43k • written 5.2 years ago by ▴ 250
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 43k • written 9.6 years ago by ▴ 100
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 43k • written 6.1 years ago by ▴ 170
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 • 0 • written 4.6 years ago by ▴ 40
6
votes
8
replies
589
views
BRAKER3 genome annotation
annotation BRAKER3 genome
updated 14 days ago by 14k • written 17 days ago by ▴ 40
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 13k • written 15 months ago by ▴ 30
6
votes
3
replies
195
views
Interpretting IGV output
IGV
updated 10 days ago by 8.7k • written 10 days ago by ▴ 30
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 43k • written 5.2 years ago by ▴ 40
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 43k • written 4.7 years ago by ▴ 60
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads illumina genome-assembly
updated 26 days ago by 43k • written 2.6 years ago by ★ 1.9k
6
votes
6
replies
4.4k
views
10x to cloupe
single-cell-transcriptomics 10x
22 days ago by firestar ★ 1.6k
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 43k • written 7.0 years ago by ▴ 80
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 43k • written 6.2 years ago by ▴ 90
5
votes
3
replies
720
views
Illumina reads preprocessing best practice for snp calling applications
Illumina snp
updated 12 days ago by • 0 • written 9 months ago by ▴ 310
5
votes
4
replies
343
views
I'm new to cell ranger. Can single cells prepared with a protocol other than the 10x genomics protocol not be processed with cell ranger?
cellranger scRNA-seq 10x
16 days ago by Spring • 0
1,101 results • Page 2 of 23
Recent Votes
Discrepancy in read counts from fastq
R: Unable to use analyzeFeatures because argument is not a vector
Comment: Odd alignment question/finding
Comment: POSSUM not working due to incompatible pssm file
Comment: Can't install AnnotationHub
C: TOPGO- how to do GO enrichment using a custom go database?
Answer: NGS forensics: how to know if data is fabricated
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Recent Replies
Comment: Bacterial plasmid analysis by shenwei356 8.4k
My colleague has an unpublished tool for plasmid analysis (clustering), and it has really good results. You might have a try. https://githu…
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…
Comment: DESeq2 processing problems 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?
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