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358 results • Page 3 of 8
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10
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1
reply
7.7k
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Tutorial: How to select reads with specific flag using samtools
next-gen-sequencing
updated 21 days ago by 39k • written 5.8 years ago by ▴ 110
12
votes
5
replies
7.7k
views
Tutorial: How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 8 weeks ago by 39k • written 7.0 years ago by ★ 9.3k
0
votes
0
replies
7.6k
views
Tutorial: Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R eviews
updated 20 days ago by 39k • written 5.4 years ago by ▴ 10
6
votes
1
reply
7.6k
views
Tutorial: Expression Analysis Of Rna-Seq Experiments With Tophat And Cufflinks
tophat RNA-seq cufflinks
updated 3 months ago by 39k • written 11.1 years ago by 98k
18
votes
22
replies
7.5k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 12 weeks ago by 39k • written 3.5 years ago by 7.9k
16
votes
11
replies
7.5k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
12 weeks ago by Ram 39k
11
votes
2
replies
7.4k
views
Tutorial: Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome plot coverage samtools
updated 27 days ago by 39k • written 6.2 years ago by ★ 1.5k
45
votes
28
replies
7.4k
views
9 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
20 days ago by Ram 39k
12
votes
0
replies
7.4k
views
Tutorial: Plot average methylation levels across TSS region
bedtools RRBS R methylation
updated 14 months ago by 39k • written 8.4 years ago by ★ 4.6k
11
votes
7
replies
7.4k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 19 days ago by 39k • written 2.3 years ago by ▴ 300
42
votes
19
replies
7.2k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 3 months ago by 39k • written 10.3 years ago by 4.1k
20
votes
2
replies
7.2k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 20 days ago by 39k • written 5.5 years ago by ★ 3.4k
6
votes
4
replies
7.0k
views
Tutorial: Overlay Multiple Tracks In Ucsc Browser [Quick Minimal Tutorial]
visualization ChIP-seq RNA-seq ucsc-genome-browser bigwig
updated 3 months ago by 39k • written 10.2 years ago by 11k
60
votes
2
replies
7.0k
views
Tutorial: Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 3 months ago by 39k • written 10.8 years ago by 98k
4
votes
2
replies
6.9k
views
Tutorial: Analyzing Genomewide Association Study Data: A Tutorial Using Plink
plink gwas
updated 3 months ago by 39k • written 11.0 years ago by 98k
64
votes
5
replies
6.8k
views
10 follow
Tutorial: Informatics of RNA-Seq.
next-gen RNA-Seq
updated 7 months ago by 39k • written 7.8 years ago by 12k
26
votes
17
replies
6.8k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv
updated 8 months ago by 39k • written 8.8 years ago by 5.9k
12
votes
11
replies
6.7k
views
Tutorial: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI Bioproject SRA BioSample
updated 28 days ago by 39k • written 6.2 years ago by ★ 2.4k
32
votes
4
replies
6.6k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 11 weeks ago by 39k • written 4.6 years ago by ★ 1.5k
49
votes
1
reply
6.6k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 3 months ago by 39k • written 2.7 years ago by 72k
15
votes
2
replies
6.5k
views
Tutorial: Genotype And Snp Calling Review Papers
snp
updated 3 months ago by 39k • written 10.8 years ago by 98k
2
votes
0
replies
6.5k
views
Tutorial: How to - Install Python packages in a virtual environment (virtualenv)
ubuntu cutadapt virtualenv python windows
updated 20 days ago by 39k • written 5.5 years ago by ▴ 310
23
votes
4
replies
6.4k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 12 weeks ago by 39k • written 3.8 years ago by 72k
15
votes
1
reply
6.4k
views
Tutorial: A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl SAM blast BED
updated 20 days ago by 39k • written 5.6 years ago by ★ 3.0k
15
votes
0
replies
6.4k
views
Tutorial: Introduction To Ngs Bioinformatics By The Bioinformatics Team At The University Of Texas
course training
updated 3 months ago by 39k • written 10.9 years ago by 98k
20
votes
5
replies
6.3k
views
Tutorial: Analysis of single-cell RNA-seq data
single-cell RNA-Seq
updated 8 weeks ago by 39k • written 6.9 years ago by ★ 1.5k
8
votes
2
replies
6.3k
views
Tutorial: Troubleshooting issues with SURPI pipeline for pathogen identification from complex metagenomic NGS data.
metagenomics clinical-genomics
updated 16 months ago by 39k • written 8.6 years ago by 12k
8
votes
12
replies
6.2k
views
Tutorial: Create your own VPN to access work resources from home
tinyproxy OpenVPN VPN
updated 8 weeks ago by 39k • written 7.0 years ago by 13k
14
votes
2
replies
6.2k
views
Tutorial: ChIP-seq analysis tutorial
ChIP-Seq
updated 9 weeks ago by 39k • written 7.8 years ago by ★ 2.9k
5
votes
5
replies
6.1k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq
updated 20 days ago by 39k • written 5.6 years ago by ▴ 130
19
votes
9
replies
6.1k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 3 months ago by 39k • written 10.0 years ago by 9.6k
6
votes
0
replies
6.0k
views
Tutorial: Leveraging Flow Order And Flow Signals From Ion Torrent Data
ion-torrent
updated 3 months ago by 39k • written 11.1 years ago by ▴ 360
29
votes
5
replies
6.0k
views
Tutorial: Gnu Parallel Tutorial
parallel gnu-parallel
updated 3 months ago by 39k • written 9.7 years ago by ★ 4.3k
4
votes
1
reply
5.9k
views
Tutorial: Chip-Seq Data Analysis Tutorial
chip-seq
updated 3 months ago by 39k • written 11.1 years ago by ▴ 360
23
votes
19
replies
5.8k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
fastq mutation cancer target
updated 8 weeks ago by 39k • written 6.7 years ago by ★ 2.4k
16
votes
6
replies
5.8k
views
Tutorial: How to make your snakefiles self-documenting
snakemake
updated 8 weeks ago by 39k • written 6.6 years ago by ★ 1.7k
20
votes
7
replies
5.7k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 12 weeks ago by 39k • written 4.6 years ago by ▴ 750
14
votes
7
replies
5.6k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 12 weeks ago by 39k • written 7.1 years ago by ★ 3.3k
22
votes
2
replies
5.6k
views
Tutorial: Use a workflow management tool to manage your computational pipelines
workflow-management snakemake pipeline
updated 8 weeks ago by 39k • written 6.6 years ago by ★ 2.1k
34
votes
4
replies
5.6k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 6 months ago by 39k • written 7.9 years ago by ▴ 370
18
votes
2
replies
5.5k
views
Tutorial: Update kraken databases
database kraken k-mer python
updated 26 days ago by 39k • written 6.1 years ago by 5.2k
6
votes
3
replies
5.4k
views
Tutorial: High Throughput Sequence Analysis With R And Bioconductor
bioconductor
updated 3 months ago by 39k • written 10.9 years ago by 98k
34
votes
15
replies
5.4k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 12 weeks ago by 39k • written 4.0 years ago by ★ 9.3k
13
votes
6
replies
5.3k
views
Tutorial: Trim & align paired-end reads in a single pass
align trim fastq pipe paired-end
updated 8 weeks ago by 39k • written 7.0 years ago by 14k
21
votes
10
replies
5.2k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 12 weeks ago by 39k • written 2.8 years ago by 12k
9
votes
2
replies
5.2k
views
Tutorial: From Data import to Normalization in Microarray Analysis using in R (Part I)
gene R
updated 8 weeks ago by 39k • written 7.0 years ago by ▴ 140
7
votes
0
replies
5.1k
views
Tutorial: Mothur Analyzing 16S Of Ngs High Through-Put Sequencing
next-gen
updated 3 months ago by 39k • written 11.0 years ago by ▴ 120
12
votes
31
replies
5.1k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 12 weeks ago by 39k • written 3.8 years ago by 7.9k
0
votes
2
replies
5.1k
views
Tutorial: Install AMOS on Ubuntu 13.10
sequencing alignment software-error next-gen
updated 19 months ago by 39k • written 8.9 years ago by 9.6k
12
votes
1
reply
5.0k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 12 weeks ago by 39k • written 3.2 years ago by 4.9k
358 results • Page 3 of 8
Recent Votes
Answer: Saving results from yeastgenome.org blastp search
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data.
Answer: Saving results from yeastgenome.org blastp search
Comment: snps from empty well, Illumina Sequencing
Extract sequences from a fastq file by a list of IDs
Answer: Extract sequences from a fastq file by a list of IDs
Answer: Differences in GTF files hg19 and hg38
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Comment: RNASeq gene labeling and mRNA filter from bulkRNA data. by Yeeshouw • 0
I see, I believe I was running an older version or have missed the option, I have updated to v2.10.5 and can see this option now. Thank you…
Answer: Saving results from yeastgenome.org blastp search by GenoMax 130k
Looks like yeastgenome site does not provide a way to export or save the results in any other format. You could do the search over at NCBI …
Answer: Differences in GTF files hg19 and hg38 by GenoMax 130k
Not sure where you got your GTF for GRCh38 from but [**one from GENCODE**][1] has the level info you are looking for. chr1 HAVANA…
Comment: CHiP-Seq Questions by B.N. • 0
Thank you for the suggestions Dr. Stark.
Comment: Diff Bind Questions by B.N. • 0
Thank you so much for the insight Dr. Stark!
Comment: Is PanCan data microarray or rna-seq by GenoMax 130k
This particular example ("GeneChip") is an array. Early TCGA samples may have been done using arrays and later sequenced. Appears to be thi…
Comment: ChatGPT optimized for bioinformatics questions by Sasha ▴ 280
Hoping to add functionality around this. Stay tuned. Big problem for our space that needs to be resolved.
Comment: Is PanCan data microarray or rna-seq by solarchan7 • 0
Hi, so this [paper](https://www.nature.com/articles/s41598-019-45165-4) uses the TCGA dataset and in the supplementary information, it ment…
Comment: counts matrix should be numeric, currently it has mode: character when using a c by Darked89 4.4k
Since the input file is named `normalized.csv` and the values look like floats most likely the counts have been already normalized somehow.
Comment: Embryo transcriptome by Basti ★ 1.6k
https://www.ebi.ac.uk/ena/browser/view/PRJEB11202 https://www.ebi.ac.uk/ena/browser/view/PRJNA153427
Comment: ChatGPT optimized for bioinformatics questions by ATpoint 72k
How is it trained on PubMed/papers? One major drawback of ChatGPT is that it wildly makes up papers that do not even exist but with great c…
Answer: sgRNA design by ATpoint 72k
gRNAs are single-stranded and by this they have a strand-specificity (depends where the PAM is) and that gives them an orientation.
Answer: counts matrix should be numeric, currently it has mode: character when using a c by ATpoint 72k
You have commas as decimal delimiters which interpreted as text. Just replace by dot and make numeric: ```r d <- data.frame(A=c("1,2", "3,…
Comment: snps from empty well, Illumina Sequencing by GenoMax 130k
> I receive illumina sequencing files with 96 wells, our lab leaves one > well empty. When I process the files with a SNP calling pipeline …
Answer: counts matrix should be numeric, currently it has mode: character when using a c by Darked89 4.4k
You can try: counts_data <- read.csv2("normalized.csv", header = TRUE) But as far as I know DESeq2 requires raw counts as inpu…
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