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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 6.8 years ago by ★ 1.3k
38
votes
24
replies
2.0k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 6 days ago by 19k • written 8 days ago by ▴ 580
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split fastq
updated 3 days ago by • 0 • written 12.8 years ago by ★ 1.7k
16
votes
12
replies
7.3k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome perl python3 bash python
updated 3 days ago by ▴ 10 • written 3.1 years ago by ▴ 120
9
votes
10
replies
503
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 3 days ago by ▴ 20 • written 4 days ago by • 0
9
votes
10
replies
584
views
High Malat-1 expression in single cell data
single-cell
updated 2 hours ago by ▴ 10 • written 7 days ago by ▴ 30
5
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon human bed v7 agilent all sureselect
updated 21 hours ago by ▴ 10 • written 24 months ago by • 0
5
votes
5
replies
272
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 3 days ago by ▴ 30 • written 4 days ago by ▴ 150
5
votes
4
replies
376
views
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
3 days ago by Estevão • 0
5
votes
5
replies
579
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 2 days ago by • 0 • written 11 days ago by ★ 3.9k
5
votes
3
replies
282
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 6 days ago by ★ 1.2k • written 6 days ago by • 0
5
votes
6
replies
524
views
Programmatically retrieving positions of protein active site residues
Uniprot PDB Proteins
updated 5 days ago by ▴ 760 • written 7 days ago by ▴ 40
4
votes
1
reply
181
views
LD-prune variants while maintaining a list of SNPs
snp vcf plink filtering independent
updated 5 hours ago by 11k • written 1 day ago by ▴ 560
4
votes
6
replies
3.7k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 1 minute ago by ▴ 30 • written 6.7 years ago by ★ 1.2k
4
votes
2
replies
207
views
GRCh38.gmap file
gnomix gmap
1 day ago by lorena9132 ▴ 10
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
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
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome sequencing singleton SNP filter
updated 6 days ago by ▴ 20 • written 9.6 years ago by ▴ 40
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
4
votes
2
replies
307
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma voom R
6 days ago by pairedttest ▴ 10
4
votes
15
replies
1.6k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR DESeq Differential-Expression RNA-Seq
updated 2 days ago by ★ 7.1k • written 4 months ago by ▴ 10
3
votes
7
replies
348
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc cutadapt illumina tile paired-end
6 days ago by salias • 0
3
votes
5
replies
267
views
Generating mpileup file using samtools
mpileup samtools
updated 3 days ago by 21k • written 3 days ago by • 0
3
votes
4
replies
324
views
Design matrix Differential expression analysis
RNA-seq Differential-expression
just now by SHN ▴ 40
3
votes
2
replies
383
views
Extract protein sequence
fasta alignment blast
5 days ago by anna ▴ 20
3
votes
0
replies
1.1k
views
Tool: Sars-Cov-2 Genome & ACE 2 Exploration
sequence alignment SNP genome
1 day ago by Ibrahim Tanyalcin ★ 1.2k
3
votes
3
replies
324
views
Is it possible to bulk download files from GEO repository?
RNA-seq Galaxy Tanscriptomics
updated 6 days ago by ▴ 580 • written 7 days ago by ▴ 750
3
votes
3
replies
315
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression RNA NOISeq DGE
updated 3 days ago by 82k • written 4 days ago by • 0
3
votes
5
replies
310
views
Converting CRAM to FastQ
GATK samtools cram SamToFastq fastq
2 days ago by Maverick ▴ 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
2
votes
2
replies
201
views
MA plot of shrunken fold change
MA-plot Deseq2
updated 6 days ago by 82k • written 6 days ago by • 0
2
votes
5
replies
931
views
Retrieval of Active site information programmatically
Catalytic Python Active PDB site Site
updated 6 days ago by ★ 2.0k • written 2.0 years ago by • 0
2
votes
2
replies
169
views
STRING-DB API can't find my protein but I can find it when I go to the STRING-DB website directly
STRING-DB protein STRING-DB-API
15 hours ago by brandon • 0
2
votes
7
replies
423
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
updated 1 day ago by ★ 1.2k • written 3 days ago by ▴ 40
2
votes
4
replies
2.6k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel gatk calling snp variant
updated 6 days ago by 9.7k • written 24 months ago by ▴ 120
2
votes
3
replies
779
views
Issues with Mixture file when using CIBERSORTx
Deconvolution CIBERSORTx
updated 1 day ago by • 0 • written 7 months ago by • 0
2
votes
2
replies
217
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 1 day ago by 43k • written 3 days ago by ▴ 30
2
votes
2
replies
260
views
Association study using SNP data
Association Allele Parentage SNP
23 hours ago by drajangirija • 0
2
votes
2
replies
1.8k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR statistical test parametric non-parametric
updated 2 days ago by ▴ 210 • written 3.8 years ago by ▴ 40
2
votes
2
replies
207
views
Raw counts using stringtie
stringtie RNA-seq
updated 2 days ago by 142k • written 2 days ago by • 0
2
votes
4
replies
294
views
from row count to tpm
tpm row-count normalization
updated 5 days ago by 43k • written 13 days ago by ▴ 20
2
votes
2
replies
2.6k
views
Pindel Segmentation Fault Error
pindel
updated 2 days ago by • 0 • written 10.2 years ago by ▴ 20
2
votes
1
reply
264
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 2 days ago by 10k • written 6 days ago by ▴ 10
2
votes
2
replies
274
views
p-value in CIBERSORT
CIBERSORT p-value
5 days ago by michelafrancesconi9 ▴ 20
2
votes
3
replies
273
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus annotation assembly genome
updated 2 days ago by ★ 1.9k • written 3 days ago by ▴ 30
1
vote
2
replies
280
views
read length in structural variant calling
nanopore SV QC ONT variant
3 days ago by eebloom ▴ 80
1
vote
2
replies
234
views
RNA-seq data for deep learning classification
rna-seq
3 days ago by yahn • 0
1
vote
1
reply
235
views
Polishing genome assembly
polishing Nanopore PacBio
updated 6 days ago by 54k • written 6 days ago by • 0
1
vote
7
replies
439
views
Downsampling long-read BAM files
nanopore BAM QC ONT downsampling
3 days ago by eebloom ▴ 80
1
vote
3
replies
280
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA illumina GEO metadata
updated 5 days ago by 142k • written 5 days ago by • 0
183 results • Page 1 of 4
Recent Votes
Comment: Design matrix Differential expression analysis
UMI-Tools 0.5, now with tools for cell barcoded scRNA-seq
Comment: install.packages("imudata")
Answer: Can I merge Hi-C fastq files from different lanes?
Answer: Interpretation of output from MiXCR TCR sequencing
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
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Recent Replies
Comment: Design matrix Differential expression analysis by SHN ▴ 40
Got it, thank you for your response. SN
Comment: How to interpret DEXseq results in therms of significance by Sara ▴ 30
Hi, I used write.table(as.data.frame(DEXSeqResults(MyObj)), "Results.tsv", quote=FALSE, sep="\t", dec=".") to save the result but I recei…
Comment: Tissue-specific DEG analysis with DEseq2 by M. ▴ 30
Can I ask what do you exactly mean by same experiment? If you are talking about the same donor and the same procedure, unfortunately, not a…
Comment: install package: package ‘gmwm’ is not available for this version of R by Ram 43k
Find someone with computer skills near you and consult them. From your posts on the forum, it's clear that you need help at a level that we…
Comment: Gene Specific coverage from WGS data by GenoMax 142k
This is not going to work no matter what program you use since the chromosome identifiers in your GTF (`MN908947.3 `) do not match your BA…
Comment: install.packages("imudata") - package ‘imudata’ is not available for this versio by Ram 43k
Read the answers in the post, understand them and try to implement them.
Comment: High Malat-1 expression in single cell data by t.montserrat.ayuso ▴ 10
Just using the normalized expression of Malat1 works.
Comment: Can I merge Hi-C fastq files from different lanes? by Winter • 0
Awesome, thank you for the concise and straight-forward answer!
Comment: error in R code by ATpoint 82k
Look, before you keep posting these sorts of questions and might gross of users, please read and follow https://www.biostars.org/p/357878/ …
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…
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