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8
votes
8
replies
695
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 11 days ago by 14k • written 12 days ago by ▴ 10
8
votes
5
replies
1.2k
views
Classifying repeat features from Ensembl
ensembl repeat
updated 20 days ago by ▴ 210 • written 16 months ago by ★ 1.4k
8
votes
16
replies
1.1k
views
How to convert plink files to Hapmap Format
GWAS Plink
updated 9 days ago by ★ 2.4k • written 8 weeks ago by • 0
8
votes
6
replies
2.5k
views
Batch effect removal with the help of sva
SVA batch-effect gene-expression
updated 27 days ago by 43k • written 3.5 years ago by ▴ 240
8
votes
10
replies
765
views
bash script
whole-genome-sequencing
updated 20 days ago by 43k • written 27 days ago by ▴ 30
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 19 days ago by 43k • written 21 months ago by ▴ 20
7
votes
7
replies
1.5k
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 20 days ago by ★ 2.5k • written 21 days ago by • 0
7
votes
2
replies
303
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 12 days ago by ▴ 390 • written 13 days ago by • 0
7
votes
3
replies
4.6k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA RNA-Seq batch-effect
updated 18 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 18 days ago by 43k • written 4.9 years ago by ▴ 30
7
votes
6
replies
541
views
Filtering sam or bam file with maximum matching region
crisper-edited alignment match
14 days ago by analyst ▴ 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 10 days ago by ▴ 850 • written 6.1 years ago by ▴ 10
7
votes
8
replies
690
views
Why are the basics so complicated? Basic coverage filtering for VCF files
filter vcf coverage
updated 23 days ago by ▴ 40 • written 26 days ago by ▴ 40
7
votes
3
replies
2.9k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 17 days ago by 6.4k • written 16 months ago by ▴ 130
7
votes
2
replies
3.7k
views
Timeout on getBM() to retrieve snps from locations
biomaRt getBM R
updated 19 days ago by 43k • written 5.2 years ago by ▴ 600
7
votes
4
replies
2.1k
views
filtering genes by pearson correlation
correlation RNA-Seq R
updated 19 days ago by 43k • written 6.1 years ago by ▴ 120
7
votes
7
replies
601
views
Can you suggest a protein PDB that has two chainst but only 50 total number of atoms?
protein pdb protein-databank
updated 23 days ago by 4.6k • written 23 days ago by • 0
7
votes
20
replies
6.5k
views
7 follow
Repeat masked gtf files from ensembl
ensembl RNA-Seq genome
updated 24 days ago by ▴ 210 • written 4.3 years ago by ▴ 80
7
votes
16
replies
738
views
How many reads for WGS Sequencing?
WGS Bacterial-Genomics
7 days ago by Ruqaiya • 0
7
votes
3
replies
1.2k
views
biomaRt::getSequence - Invalid type argument
biomaRt R
updated 19 days ago by 43k • written 3.9 years ago by ▴ 690
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 19 days ago by 43k • written 2.0 years ago by ▴ 60
7
votes
7
replies
1.1k
views
Prediction tools summary - zero values
statistics
updated 19 days ago by • 0 • written 6 months ago by ▴ 50
6
votes
4
replies
1.5k
views
RNA-Seq: X samples and X batches
RNA-Seq edgeR DESeq2 Batch-Effect
updated 19 days ago by 43k • written 5.2 years ago by ▴ 40
6
votes
6
replies
4.4k
views
10x to cloupe
single-cell-transcriptomics 10x
26 days ago by firestar ★ 1.6k
6
votes
3
replies
206
views
Interpretting IGV output
IGV
updated 13 days ago by 8.7k • written 14 days ago by ▴ 30
6
votes
2
replies
1.5k
views
Writing a batch script for analyzing RNA-Seq data
RNA-Seq quantification alignment
updated 19 days ago by 43k • written 5.2 years ago by ▴ 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 17 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 18 days ago by • 0 • written 4.6 years ago by ▴ 40
6
votes
11
replies
3.4k
views
Collapsing probesets to genes on WGCNA
WGCNA gene-expression R
updated 19 days ago by 43k • written 5.3 years ago by ▴ 120
6
votes
10
replies
2.3k
views
Why different DEGs between my result and the author's result?
limma microarray differential-gene-expression
updated 26 days ago by 43k • written 6.1 years ago by ▴ 170
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma microarray DEA batch-effect
updated 18 days ago by 43k • written 4.7 years ago by ▴ 60
6
votes
0
replies
208
views
Herald: The Biostar Herald for Monday, April 15, 2024
herald
20 days ago by Biostar 2.7k
6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna RNA-Seq ChIP-Seq
updated 27 days ago by • 0 • written 3.9 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 19 days ago by 43k • written 9.6 years ago by ▴ 100
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat RNA-Seq Limma DESeq2 batch-effect
updated 17 days ago by 43k • written 5.0 years ago by ▴ 140
6
votes
8
replies
615
views
BRAKER3 genome annotation
annotation BRAKER3 genome
updated 18 days ago by 14k • written 21 days ago by ▴ 40
5
votes
4
replies
357
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
19 days ago by Spring • 0
5
votes
14
replies
1.0k
views
Not getting any modification calls in nanopore reads with dorado basecaller
mofications dorado basecalling nanopore methylation
updated 24 days ago by 142k • written 6 weeks ago by ▴ 20
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
updated 25 days ago by • 0 • written 3.8 years ago by ★ 1.8k
5
votes
2
replies
1.8k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq batch batch-effect sequencing
updated 19 days ago by 43k • written 3.0 years ago by ▴ 60
5
votes
4
replies
2.2k
views
How do we process Kallisto output (continuous real values) for DESEQ2 analysis (which strictly require discrete count values)?
read-counts DESEQ2 differential-gene-expression kallisto
updated 26 days ago by 43k • written 2.7 years ago by ▴ 170
5
votes
13
replies
9.2k
views
8 follow
biomaRt: Timeout on getBM().
r biomart ensembl
updated 24 days ago by ★ 2.0k • written 2.8 years ago by ▴ 40
5
votes
2
replies
672
views
DESeq2- How to design data for multiple comparisons?
Differential-Gene-Expression RNA-Seq DESeq2 R
updated 26 days ago by 43k • written 3.6 years ago by • 0
5
votes
3
replies
282
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 5 days ago by ★ 1.2k • written 6 days ago by • 0
5
votes
13
replies
1.6k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 15 days ago by 82k • written 16 days ago by ★ 1.7k
5
votes
4
replies
687
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq EdgeR DEGs DESeq2
17 days ago by BioinfGuru ★ 1.7k
5
votes
5
replies
268
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 3 days ago by ▴ 30 • written 3 days ago by ▴ 150
5
votes
5
replies
571
views
NCBI MEGABLAST versus UCSC BLAT
blast blat alignment megablast
updated 26 days ago by ▴ 580 • written 27 days ago by ▴ 40
5
votes
3
replies
412
views
Ensembl assembly choice for DNA reference with no combined primary assembly
alignment HISAT2 RNA-Seq ensembl Assembly
updated 24 days ago by 142k • written 24 days ago by ▴ 20
5
votes
3
replies
339
views
Best genome browser for manual curation of gene structure(s)?
structure gene
updated 24 days ago by ★ 3.8k • written 25 days ago by ★ 5.3k
961 results • Page 2 of 20
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Answer: ERROR When Using Ensembl Plants Biomart Wget API
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Answer: STRING-DB API can't find my protein but I can find it when I go to the STRING-DB
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mitochondria in single nuclear RNAseq
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Recent Replies
Comment: install.packages("imudata") by zx8754 11k
[How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning?](https://stackoverflow.com/q/25721884/680068)
Answer: install.packages("imudata") by ATpoint 82k
Welcome to this community. Please learn the most important lesson right away which is reading answers and learning from it. Users gave you …
Comment: install.packages("imudata") by marco.barr ▴ 90
You can install from github directly. Many R packages are not present in the CRAN repository or in Bioconductor( from Biocmanager). Also re…
Comment: install package by snajafy • 0
Hi, Thanks for your answer, I do it, but I get this error: ERROR: compilation failed for package 'gmwm' removing 'C:/Users/najafi/AppData/…
Comment: Quetion regarding WGCNA by andres.firrincieli 3.6k
There is something wrong with your data but without any context I can't really answer to your question. I would like to see a PCA plot of …
Comment: error to run rnammer by antonio.spl • 0
please could you tell me what was the solution, I am having the same problem, I only get empty files.
Comment: install package by snajafy • 0
Hi, Thanks for your answer, I do it, but I get this error: ERROR: compilation failed for package 'gmwm' * removing 'C:/Users/najafi/AppData…
Answer: Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so t by swbarnes2 14k
Any chance the numerical columns were imported as factors?
Comment: ERROR When Using Ensembl Plants Biomart Wget API by Dora ▴ 10
Thank you very much, that works perfectly :) ! Maybe someone needs to use a plant dataset as an example (instead of human dataset ) in the …
Comment: Truncated Bam Error by guanghao • 0
I also have this problem, but it doesn't work even I remove the Xms32g. The result bam is still malformed.
Answer: DMRcate ranges liftover hg19 to hg38 by aaron.stevens • 0
Hey, I believe they are mapped to hg19 and this is potentially a bigger problem than people realise, I nearly made this mistake and I would…
Comment: STRING-DB API can't find my protein but I can find it when I go to the STRING-DB by brandon • 0
This worked beautifully using 'requests.get()' in python, thank you so much!
Answer: STRING-DB API can't find my protein but I can find it when I go to the STRING-DB by Pierre Lindenbaum 161k
first get the main ID in stringdb: $ wget -qO - "https://string-db.org/api/tsv-no-header/get_string_ids?identifiers=RPS4Y1&species=960…
Comment: Help with DGEList function by marco.barr ▴ 90
Are you sure you've loaded the library properly? Have you checked if edgeR is ticked in the list of installed packages? Double-check it. If…
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…
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