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963 results • Page 2 of 20
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9
votes
10
replies
501
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 3 days ago by ▴ 20 • written 4 days ago by • 0
4
votes
10
replies
1.5k
views
Do I have batch effect?
RNA-Seq edgeR batch-effect
updated 20 days ago by 43k • written 3.9 years ago by ▴ 20
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma sva Combat batch-effect
updated 6 days ago by ▴ 40 • written 6.7 years ago by ★ 1.3k
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 19 days ago by 43k • written 7.4 years ago by • 0
9
votes
10
replies
4.4k
views
Using rnaseq reference sample across batches
RNA-Seq batch-effect
updated 19 days ago by 43k • written 7.4 years ago by ▴ 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 19 days ago by 43k • written 2.0 years ago by ▴ 60
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 17 days ago by 43k • written 4.6 years ago by ▴ 140
3
votes
10
replies
669
views
Piping samtools to R
R NGS bash samtools
19 days ago by noodle ▴ 580
1
vote
10
replies
4.0k
views
Error in CIBERSORTx
RNA-seq CIBERSORT LM22
updated 21 days ago by ▴ 330 • written 19 months ago by • 0
1
vote
10
replies
1.0k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq DESeq2 DNA-contamination
11 days ago by DKA ▴ 40
0
votes
10
replies
526
views
Low mapping rate with Salmon
RNA-seq Salmon Quantification
updated 6 days ago by 19k • written 13 days ago by • 0
13
votes
10
replies
6.4k
views
Adjusting for confounding variables in RNA-SEQ Differential Expression Analysis
Differential-Gene-Expression RNA-Seq Statistics
updated 26 days ago by 43k • written 5.7 years ago by ▴ 40
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
2
votes
9
replies
908
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 12 days ago by 4.2k • written 6 months ago by • 0
0
votes
9
replies
634
views
99.9999% of Q30 bases is normal?
RNA-seq fastp
updated 24 days ago by 4.2k • written 25 days ago by ▴ 20
1
vote
9
replies
4.7k
views
Help with multiple batch effects
sva combat batch-effect
updated 19 days ago by 43k • written 5.9 years ago by ▴ 30
9
votes
9
replies
560
views
High Malat-1 expression in single cell data
single-cell
updated 1 day ago by 43k • written 6 days ago by ▴ 30
11
votes
9
replies
7.0k
views
How to choose method to integrate different patient sample together in Seurat
Seurat scRNA batch-effect harmony
updated 18 days ago by 43k • written 4.2 years ago by ▴ 80
1
vote
9
replies
1.2k
views
Supergnova stuck in tutorial
Genetic Correlations Python Supergnova Conda
updated 18 days ago by • 0 • written 19 months ago by ▴ 10
4
votes
9
replies
2.7k
views
Tool: CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.3 years ago by • 0
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling single-cell scRNA-seq batch-effect
updated 19 days ago by 43k • written 3.9 years ago by ▴ 20
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome base-calling fastq nanopore
updated 7 days ago by 43k • written 8 months ago by • 0
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly statistics
updated 23 days ago by • 0 • written 4.7 years ago by ▴ 10
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference 38build impute imputation
6 days ago by anna ▴ 20
3
votes
9
replies
896
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 17 days ago by ★ 2.4k • written 18 days ago by • 0
3
votes
9
replies
541
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 11 days ago by 100k • written 13 days ago by • 0
4
votes
9
replies
2.1k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing bowtie2 alignment samtools ngs
updated 2 days ago by • 0 • written 2.2 years ago by • 0
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
8
votes
8
replies
698
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 11 days ago by 14k • written 12 days ago by ▴ 10
3
votes
8
replies
4.1k
views
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
fpkm scRNA-seq RNA-Seq tpm batch-effect
updated 17 days ago by 43k • written 4.6 years ago by ▴ 180
0
votes
8
replies
441
views
What does it mean single base resolution in sequencing?
SNP sequencing
updated 5 days ago by 4.2k • written 7 days ago by ▴ 10
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport
updated 3 days ago by • 0 • written 5.1 years ago by 11k
3
votes
8
replies
1.3k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq Cellranger STARsolo 10X
updated 16 days ago by 14k • written 9 months ago by ▴ 80
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing software-error RNA-seq
updated 26 days ago by • 0 • written 4.7 years ago by ▴ 180
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
3
votes
8
replies
5.0k
views
An idea to identify batch effects
microarray batch-effect
updated 17 days ago by 43k • written 9.7 years ago by • 0
4
votes
8
replies
674
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
updated 9 days ago by 35k • written 10 days ago by ▴ 10
0
votes
8
replies
399
views
Error in cnetplot enrichplot package
R
updated 13 days ago by 43k • written 13 days ago by • 0
1
vote
8
replies
479
views
Downsampling fastq file
downsample fastq
5 days ago by marco.barr ▴ 90
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression RNA-seq gene-ontology
updated 26 days ago by 43k • written 6.5 years ago by ★ 1.6k
1
vote
8
replies
905
views
Adding CB tag to bam file
samtools bam
updated 11 days ago by 161k • written 17 days ago by • 0
1
vote
8
replies
3.5k
views
Best way to address different batches of RNA-seq
sequence RNA-Seq RPKM Fold-Change batch-effect
updated 18 days ago by 43k • written 7.0 years ago by ▴ 20
6
votes
8
replies
615
views
BRAKER3 genome annotation
annotation BRAKER3 genome
updated 19 days ago by 14k • written 21 days ago by ▴ 40
1
vote
8
replies
710
views
6 follow
Finding insert sequences using long reads
insert-sequences Nanopore long-read-assembly
updated 26 days ago by ▴ 630 • written 8 weeks ago by ▴ 20
4
votes
7
replies
591
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
6 days ago by e.r.zakiev ▴ 210
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
10
votes
7
replies
7.1k
views
6 follow
Convert GVF to VCF
vcf
updated 20 days ago by • 0 • written 9.3 years ago by ▴ 970
3
votes
7
replies
1.0k
views
Can I use batch effect correction "by parts"?
ComBat RNA-Seq batch-effect
updated 18 days ago by 43k • written 4.3 years ago by ▴ 360
3
votes
7
replies
521
views
Integration of transcriptomics and proteomics: difficult matching names
rna-seq tmt nomenclature proteomics
19 days ago by ntsopoul ▴ 60
2
votes
7
replies
906
views
Removing duplicates
duplicates ONT minimap2
updated 17 days ago by ▴ 580 • written 18 days ago by • 0
963 results • Page 2 of 20
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Recent Replies
Comment: Gene Specific coverage from WGS data by 1769mkc ★ 1.2k
"Also if is there any other quick way to find gene specific coverage" can you give some example so that its bit more clear what do you mean…
Answer: Tissue-specific DEG analysis with DEseq2 by ATpoint 82k
I assume that all data are from the same experiment, without batch effects and can thus be quantitiatively compared: Many ways to do thi…
Comment: install.packages("imudata") - package ‘imudata’ is not available for this versio by snajafy • 0
I am facing the same problem and I don't know how to solve the problem,....
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!
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