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6,853 results • Page 4 of 138
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Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 8 months ago by 148k • written 8 months ago by • 0
22
votes
14
replies
30k
views
7 follow
removing batch effects using ComBat and SVA
SVA ComBat R Batch-effect
updated 9 months ago by 44k • written 8.6 years ago by ▴ 280
36
votes
14
replies
2.3k
views
9 follow
Forum: Good Bioinformatics Jokes/Puns?
bioinformatics
updated 6 months ago by 12k • written 7 months ago by ▴ 20
10
votes
14
replies
7.3k
views
8 follow
Coverage plot of a complete genome
coverage plot CNV
updated 5 months ago by ▴ 20 • written 4.2 years ago by ▴ 10
17
votes
14
replies
9.9k
views
Using featureCounts and DESeq2 to look at differences between ATAC-seq conditions.
ATAC-seq next-gen R
updated 5 months ago by ▴ 70 • written 6.3 years ago by ▴ 350
1
vote
14
replies
1.3k
views
Deseq2 , Limma - the paired test seems to be incorrect - is it known problem ?
deseq
updated 7 months ago by 21k • written 7 months ago by ▴ 220
2
votes
14
replies
1.2k
views
FastQC GC-content, bimodal for maize?
RNA-seq
6 months ago by boczniak767 ▴ 870
12
votes
14
replies
3.0k
views
8 follow
Forum: Recovering bam files after unknown deletion in the storage
photorec bam sequencing
written 5.6 years ago by ▴ 70
31
votes
14
replies
12k
views
11 follow
Finding Rrna Genes In Metagenomic Data
rna rRNA metagenomics
updated 10 months ago by 44k • written 14.3 years ago by ▴ 650
16
votes
14
replies
16k
views
9 follow
Combining GSEA (Gene Set Enrichment analysis) and DEG (Differentially Expressed Genes) to confirm results together- is it a good idea?
RNA-Seq R sequencing
updated 3 months ago by • 0 • written 4.5 years ago by ▴ 30
0
votes
14
replies
1.6k
views
DEseq2 on expected counts
DEseq2 Normalize raw-counts
updated 5 months ago by 88k • written 5 months ago by ▴ 10
0
votes
14
replies
1.3k
views
frma normalization
affybatch frma mcp-counter
11 months ago by michelafrancesconi9 ▴ 20
1
vote
14
replies
1.7k
views
Bowtie alignment
Bowtie2 singletons
11 months ago by daffodil ▴ 10
4
votes
14
replies
3.1k
views
7 follow
Is there anyone who downloaded Azimuth packges?
Azimuth scRNAseq
updated 6 weeks ago by 86k • written 10 months ago by ▴ 20
5
votes
14
replies
2.7k
views
Not getting any modification calls in nanopore reads with dorado basecaller
mofications dorado basecalling nanopore methylation
updated 9 months ago by 148k • written 10 months ago by ▴ 20
13
votes
14
replies
2.3k
views
High Malat-1 expression in single cell data
single-cell
updated 8 months ago by ▴ 40 • written 9 months ago by ▴ 50
9
votes
14
replies
1.7k
views
Proper reanotation of genepanel with snpEff and dbNSFP
vcf
5 months ago by Lukas ▴ 130
3
votes
14
replies
1.6k
views
vg installation on MacOS failing: "ld: -headerpad: not a hexadecimal number: -headerpad_max_install_names"
macos vg
updated 6 months ago by 148k • written 6 months ago by ▴ 10
2
votes
14
replies
1.1k
views
convert list to fasta format
python
updated 6 months ago by 44k • written 6 months ago by ▴ 100
7
votes
14
replies
799
views
Proteomics data analysis
data-analysis biostatistics statistics proteomics
11 days ago by Ariadna ▴ 20
31
votes
14
replies
25k
views
7 follow
Difference between tSNE and PCA analysis
next-gen rna-seq
updated 11 months ago by 23k • written 7.0 years ago by ▴ 160
6
votes
14
replies
3.2k
views
Reheadering a subsetted bam gives truncated file
samtools bam
updated 6 months ago by ▴ 280 • written 6.5 years ago by • 0
4
votes
14
replies
6.0k
views
Trouble with bedtools getfasta
bedtools getfasta
written 3.0 years ago by ▴ 30
2
votes
14
replies
2.1k
views
jellyfish installed in conda, but 'command not found' when I try to run it
jellyfish conda
updated 11 months ago by 22k • written 11 months ago by ▴ 200
2
votes
14
replies
3.8k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 8 months ago by ▴ 10 • written 5.5 years ago by ▴ 60
17
votes
14
replies
9.7k
views
11 follow
how to split multi-fasta file into single fasta file named by header
genome perl python3 bash python
updated 7 months ago by 8.7k • written 3.8 years ago by ▴ 120
7
votes
14
replies
3.7k
views
6 follow
How to find tandem duplications pattern in a DNA sequence
Repeat
updated 8 months ago by ▴ 30 • written 3.8 years ago by • 0
4
votes
13
replies
1.3k
views
Can't reproduce harmony results in Seurat
Seurat scRNA-seq harmony
4 months ago by fifty_fifty ▴ 70
36
votes
13
replies
7.8k
views
8 follow
How Do You Log Details Of Data Processing/ Pipelines / In Silico Analyses Performed
data galaxy
written 13.7 years ago by ▴ 520
25
votes
13
replies
1.3k
views
6 follow
Forum: How to do datamining in bioinformatics
data-mining
updated 3 months ago by 4.5k • written 3 months ago by ▴ 70
7
votes
13
replies
5.6k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 9 months ago by 86k • written 9 months ago by ★ 2.1k
4
votes
13
replies
1.4k
views
BBMap Excess Fold Coverage
bbmap
updated 6 months ago by 148k • written 7 months ago by • 0
6
votes
13
replies
5.3k
views
11 follow
ADMIXTURE Segmentatio fault
admixture plink vcf
updated 10 weeks ago by ▴ 20 • written 3.6 years ago by ▴ 40
6
votes
13
replies
1.4k
views
Allocating right resources to HPC using LSF scheduler
BWA GATK hpc lsf bsub
10 months ago by Maverick ▴ 10
9
votes
13
replies
1.2k
views
How do i calculate the mean of triplicates in a data.frame based on pattern?
tidyverse r
updated 7 months ago by ▴ 220 • written 8 months ago by ★ 1.9k
4
votes
13
replies
2.1k
views
7 follow
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
DEG limma rstudio
updated 7 months ago by 148k • written 8 months ago by ▴ 60
1
vote
13
replies
1.2k
views
Error with plotMDS in R
plotMDS RStudio
6 months ago by egascon ▴ 60
10
votes
13
replies
3.6k
views
Seeking feedback on ChIP-seq normalization method: Calculating scaling factors by dividing input by IP, including spike-in
ChIP-seq spike-in scaling-factor coverage
5 months ago by kalavattam ▴ 280
9
votes
13
replies
5.6k
views
Custom Reference panel creation for data imputation from .vcf files
imputation reference panel
updated 8 months ago by ▴ 50 • written 7.1 years ago by ▴ 500
9
votes
13
replies
1.2k
views
7 follow
Nextflow process not executing
STAR-mapping. Nextflow
6 months ago by myoui3122010 ▴ 30
5
votes
13
replies
2.8k
views
6 follow
GATK memory error with Java
GATK VCF SNP Java
6 months ago by anikcropscience ▴ 260
2
votes
13
replies
5.2k
views
8 follow
scatter plot for DAPC
snp
updated 4 months ago by ▴ 30 • written 5.4 years ago by ▴ 230
12
votes
13
replies
7.0k
views
7 follow
Centrimo error: Template does not contain data section
ChIP-Seq MEME
updated 7 months ago by ▴ 70 • written 5.3 years ago by ▴ 70
9
votes
13
replies
2.3k
views
7 follow
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 8 months ago by 21k • written 9 months ago by ▴ 10
10
votes
13
replies
1.2k
views
undermined fastq and top unknown barcodes
bcl2fastq
updated 5 weeks ago by 148k • written 6 weeks ago by ★ 1.2k
75
votes
13
replies
68k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
classification r cancer randomForest machine-learning
updated 5 months ago by 20k • written 11.2 years ago by ★ 1.2k
12
votes
13
replies
12k
views
11 follow
how to use ESTIMATE to infer tumor purity and stromal score from RNA-seq data?
rna-seq
updated 3 months ago by • 0 • written 7.3 years ago by ▴ 80
4
votes
13
replies
1.0k
views
Mouse genome featureCounts
GRCm39 RNA-seq featureCounts
16 days ago by rajdeepboral00 ▴ 20
13
votes
13
replies
19k
views
9 follow
How Do I Translate Multiple (More Than 25000) Dna Sequences With Different Frames To Protein Seuquence?
dna protein
updated 9 months ago by • 0 • written 11.1 years ago by ▴ 170
4
votes
13
replies
1.6k
views
RNAseq of primary tumor and metastases in two different organ
metastases RNA-seq DEG R
updated 9 months ago by ★ 2.1k • written 9 months ago by • 0
6,853 results • Page 4 of 138
Recent Votes
Sylamer analysis for detecting microRNA binding
Answer: Error from Using FindVariableFeatures Function in Seurat Package
Answer: On applying spike-in-derived scaling factors to ChIP-seq data: adjust for backgr
Answer: How to download FASTQ files from the European Nucleotide Archive (ENA) to use th
Answer: SRA fastq modify by 10x valid fastq
Combining two fasta sequences into one
A: Combining two fasta sequences into one
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Recent Replies
Comment: Error from Using FindVariableFeatures Function in Seurat Package by Binghong ▴ 20
Thanks for your guidance, I have a try!
Comment: WGCNA: Can we use high power for signed network? by Crystal571 • 0
I used to do that to my TPM, but I got some negative values in my matrix after removebatcheffect. Is that reasonable?
Comment: 16S SILVA with Kraken2 doesn't classfying at species level by Aytaç • 0
I have tried. Problem is in SILVA's naming and coding the seqeunces. They have code and species level in one of their file which is from NC…
Comment: PacBio long read processing by GenoMax 148k
ONT has similar workflows. This is probably what you need https://github.com/epi2me-labs/wf-transcriptomes
Comment: Fast, flexible grep for very large FASTQ files by milesforjazz ▴ 70
v.1.4.2 introduced the ability to enumerate variants. Read the preprint at **bioRxiv**: https://doi.org/10.1101/2025.01.09.632104
Comment: PacBio long read processing by Mai.Nabil • 0
oh, that's great. I want to do isoform quantification. Also, does Oxford Nanopore have a different workflow?
Answer: Protein adnotation, gene adnnotation, hordeum vulgare RNA-Seq by GenoMax 148k
UniProt appears to have proteomes for Barley: https://www.uniprot.org/proteomes/UP000011116 That may be your best bet. They also have GO a…
Comment: Protein adnotation, gene adnnotation, hordeum vulgare RNA-Seq by Pierre Lindenbaum 165k
there is a biomart for your genome http://plants.ensembl.org/index.html but I'm afraid the annotation for GO are empty, and KEGG is missing…
Answer: On applying spike-in-derived scaling factors to ChIP-seq data: adjust for backgr by kalavattam ▴ 280
Yes, one should account for background signal with input—although many studies do not. For more details, see [Patel et al., The Wild West o…
Comment: 16S SILVA with Kraken2 doesn't classfying at species level by noodle ▴ 620
Can you just use nt? Or grab the species level info from nt that you get hits for in the 16S databases and remap? I would expect the 16S d…
Comment: WGCNA: Can we use high power for signed network? by ATpoint 86k
18 is below what the authors recommend. TPM has nothing to do with covariantes, and yes you can regress batch from TPM.
Answer: WGCNA: Can we use high power for signed network? by Crystal571 • 0
1.I think your deepsplit and minmodulesize are too low. I had 18 samples with 18000 genes and I also used vst and removebatcheffects, but I…
Comment: SRA fastq modify by 10x valid fastq by wyuan37 • 0
Thank you! The Data Access is really helpful!
Comment: ribosomeProfilingQC help by tommy ▴ 40
Hello, Jack. Thanks for taking the time to answer my question. I believe my dataset should be valid, as I downloaded it directly from [jour…
Answer: Integration of Cut&Tag to ATACseq and RNAseq data - impact of a mutation by LChart 4.7k
It seems to me you're thinking mechanistically about this PU.1 mutation. In general it is hard to disentangle direct effects (PU.1 -> Acces…
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