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1,000 results • Page 2 of 20
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9
votes
4
replies
271
views
Ubuntu storage space is decreasing automatically
ubuntu storage
updated 16 days ago by 6.4k • written 16 days ago by ▴ 30
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 43k • written 4.5 years ago by ▴ 140
8
votes
15
replies
704
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 1 hour ago by 141k • written 7 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
8 days ago by Ram 43k
8
votes
2
replies
772
views
News: FINAL CALL - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (May 6-8, 2024 in Berlin)
single-cell sequencing
20 days ago by David Langenberger 11k
8
votes
3
replies
358
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 ▴ 60
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 3.0k • written 24 months ago by ▴ 230
8
votes
4
replies
3.0k
views
Read count correlation between samples
differential-gene-expression RNA-seq
updated 16 days ago by 43k • written 6.5 years ago by ★ 1.6k
8
votes
5
replies
1.2k
views
Classifying repeat features from Ensembl
ensembl repeat
updated 10 days ago by ▴ 200 • written 16 months ago by ★ 1.4k
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 43k • written 3.5 years ago by ▴ 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 22 days ago by • 0 • written 3.4 years ago by ▴ 40
8
votes
10
replies
698
views
bash script
whole-genome-sequencing
updated 10 days ago by 43k • written 17 days ago by ▴ 30
8
votes
6
replies
615
views
The bioinformatics paper reappears, but the results are significantly different from the original results
reproducibility
21 days ago by jiao ▴ 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 9 days ago by 43k • written 2.0 years ago by ▴ 60
7
votes
3
replies
1.2k
views
biomaRt::getSequence - Invalid type argument
biomaRt R
updated 8 days ago by 43k • written 3.8 years ago by ▴ 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 10 days ago by ★ 2.5k • written 11 days ago by • 0
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 ▴ 40 • written 16 days ago by ▴ 40
7
votes
8
replies
662
views
6 follow
How to BLAST more than 5 sequences against UniProt database?
BLAST Protein UniProt
21 days ago by Riq ▴ 50
7
votes
6
replies
462
views
Filtering sam or bam file with maximum matching region
crisper-edited alignment match
4 days ago by analyst ▴ 30
7
votes
7
replies
1.0k
views
Prediction tools summary - zero values
statistics
updated 9 days ago by • 0 • written 6 months ago by ▴ 50
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 43k • written 21 months ago by ▴ 20
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq SNP
updated 11 hours ago by ▴ 850 • written 6.1 years ago by ▴ 10
7
votes
4
replies
2.1k
views
filtering genes by pearson correlation
correlation RNA-Seq R
updated 8 days ago by 43k • written 6.1 years ago by ▴ 120
7
votes
4
replies
1.9k
views
AlphaFold 2 alternatives
protein-structure alphafold
updated 23 days ago by 43k • written 17 months ago by ★ 2.5k
7
votes
7
replies
549
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 4.5k • written 13 days ago by • 0
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 43k • written 4.8 years ago by ▴ 30
7
votes
3
replies
2.8k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 6 days ago by 6.4k • written 15 months ago by ▴ 130
7
votes
2
replies
3.7k
views
Timeout on getBM() to retrieve snps from locations
biomaRt getBM R
updated 8 days ago by 43k • written 5.2 years ago by ▴ 600
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 43k • written 5.1 years ago by ▴ 100
7
votes
20
replies
6.4k
views
7 follow
Repeat masked gtf files from ensembl
ensembl RNA-Seq genome
updated 14 days ago by ▴ 200 • written 4.3 years ago by ▴ 80
7
votes
2
replies
255
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 2 days ago by ▴ 390 • written 3 days ago by • 0
6
votes
8
replies
544
views
BRAKER3 genome annotation
annotation BRAKER3 genome
updated 8 days ago by 14k • written 10 days ago by ▴ 40
6
votes
9
replies
1.8k
views
How to convert .wib files to .wig or .bed?
wib BED wig bedtools
29 days ago by Zeng Jingyu ▴ 60
6
votes
6
replies
4.3k
views
10x to cloupe
single-cell-transcriptomics 10x
16 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 43k • written 5.1 years ago by ▴ 250
6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna RNA-Seq ChIP-Seq
updated 17 days ago by • 0 • written 3.9 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 7 days ago by 43k • written 4.9 years ago by ▴ 140
6
votes
4
replies
1.5k
views
RNA-Seq: X samples and X batches
RNA-Seq edgeR DESeq2 Batch-Effect
updated 8 days ago by 43k • written 5.2 years ago by ▴ 40
6
votes
11
replies
3.3k
views
Collapsing probesets to genes on WGCNA
WGCNA gene-expression R
updated 8 days ago by 43k • written 5.2 years ago by ▴ 120
6
votes
17
replies
6.6k
views
Can you add a label key to heatscatter plot in R?
heatscatter visualization R
updated 8 days ago by 43k • written 9.6 years ago by ▴ 100
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 43k • written 4.7 years ago by ▴ 60
6
votes
3
replies
173
views
Interpretting IGV output
IGV
updated 3 days ago by 8.7k • written 3 days ago by ▴ 30
6
votes
0
replies
190
views
Herald: The Biostar Herald for Monday, April 15, 2024
herald
10 days ago by Biostar 2.7k
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 43k • written 6.1 years ago by ▴ 170
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads illumina genome-assembly
updated 20 days ago by 43k • written 2.6 years ago by ★ 1.9k
6
votes
13
replies
602
views
Variant calling of GBS data
GBS variants BQSR
28 days ago by analyst ▴ 30
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 43k • written 7.0 years ago by ▴ 80
6
votes
4
replies
2.2k
views
Is there a way to get RNAFold output for multifasta in tabular format?
RNAFold
updated 8 days ago by • 0 • written 4.6 years ago by ▴ 40
5
votes
2
replies
1.0k
views
How to perform batch correction when we have only single condition?
sva combat batch-effect DESeq2
updated 9 days ago by 43k • written 3.8 years ago by ▴ 680
1,000 results • Page 2 of 20
Recent Votes
Answer: Seurat merge and batch correction
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Comment: How to convert plink files to Hapmap Format
Answer: Missing protein (VEGF-A) in String db
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Recent Replies
Comment: Missing protein (VEGF-A) in String db by shalespringer • 0
Thank you for replying here; this helped me figure out why MAPK10 was missing from my results. It was also marked as a pseudogene in the En…
Comment: How to convert plink files to Hapmap Format by Sofia • 0
These are the first lines of the output: (Please is it normal to have NA in the P value column ?) CHR …
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by atowns21 • 0
So I used the barcodes that I created (combos of positions 1-10 and 11-20) and I obtained similar alignment stats as the paper I pulled the…
Comment: How to convert plink files to Hapmap Format by Sofia • 0
Thank you so much, it actually worked!
Answer: Rare Disease Variant Pathway Analysis by LauferVA 4.2k
Hi @efc1e545 , First a caveat. the information we most need in order to help guide you to a successful conclusion is not provided in thi…
Answer: Sequence read length shorter than flow cell specification by swbarnes2 14k
The company probably had you share your run with someone who needed the extra bases. So you get the extra bases free. Just use them unle…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by Ram 43k
Thank you, the `csvtk spread` is super useful. I usually import into R using `lapply` then `Reduce` using `merge` but this might be easier.
Comment: Annovar using R package by DKA ▴ 40
Thank you for your guidance. The thing is that I am unfamiliar with using such environments, unfortunately.
Comment: Treatment VS Control in Single Cell RNAseq analysis by ATpoint 82k
Open a new question, with details.
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets by ATpoint 82k
I recommend https://bioconductor.org/books/3.18/OSCA.basic/normalization.html as well as the "advanced" section in this book.
Comment: Why gatk VariantAnnotator required bam and coverage files by QX • 0
thank you!
Comment: Treatment VS Control in Single Cell RNAseq analysis by kilcdincer ▴ 10
Hello, I have more or less same experimental setting and was wondering how you proceeded with your analysis? Can I reach its GitHub reposit…
Comment: BLAST using both nucleotides and taxonomic local databases by GenoMax 141k
> I ask this as some BLAST command fields as scinames or sblastnames do not give any output with a classic nt BLAST If that information is…
Answer: BLAST using both nucleotides and taxonomic local databases by 5heikki 11k
This has been discussed [many times][1] [1]: https://www.biostars.org/p/76551/
Answer: why renaming Idents in Seurat object doesn't work? by Bioinfotec ▴ 10
I think when you give indent to seuObj : ```r Idents(seuObj) <- 'RNA_snn_res.0.1' ``` You may wrongly assign other value to it such as `…
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