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411 results • Page 4 of 9
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Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy R
updated 13 months ago by 43k • written 6.1 years ago by ★ 4.0k
6
votes
3
replies
4.5k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment sequencing RNA-seq gene
updated 13 months ago by 43k • written 5.5 years ago by ▴ 40
6
votes
3
replies
5.7k
views
Tutorial: High Throughput Sequence Analysis With R And Bioconductor
bioconductor
updated 14 months ago by 43k • written 11.8 years ago by 100k
9
votes
3
replies
4.2k
views
Tutorial: Ht Sequence Analysis With R And Bioconductor By The Bioinformatics Center At Uc Riverside
bioconductor
updated 14 months ago by 43k • written 11.7 years ago by 100k
5
votes
3
replies
5.4k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 13 months ago by • 0 • written 6.5 years ago by ▴ 130
2
votes
3
replies
564
views
Tutorial: Bulk RNA-seq: Different Expression Analysis with DEseq2
python pyDESeq2 RNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
3
votes
3
replies
2.8k
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC TCGABiolinks STAR
updated 14 months ago by 43k • written 2.0 years ago by ★ 4.3k
3
votes
3
replies
8.8k
views
Tutorial: High Speed Downloading of SRA, SAM and Fastq Files
fastq sam Aspera-Connect sra
updated 11 months ago by 43k • written 6.3 years ago by ▴ 100
5
votes
3
replies
4.2k
views
Tutorial: Chip Seq Review Papers
chip-seq
updated 14 months ago by 43k • written 11.4 years ago by ▴ 80
1
vote
3
replies
3.2k
views
Tutorial: resolving error of sspace_standard
software-error Assembly
updated 12 months ago by 43k • written 7.7 years ago by ▴ 300
74
votes
3
replies
39k
views
Tutorial: Revisiting the FastQC read duplication report
fastqc
updated 2.4 years ago by 43k • written 9.8 years ago by 100k
7
votes
3
replies
2.5k
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
updated 12 months ago by ▴ 110 • written 20 months ago by 87k
50
votes
3
replies
4.8k
views
Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 13 months ago by 43k • written 5.3 years ago by 82k
16
votes
3
replies
4.3k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 3.1 years ago by • 0 • written 3.6 years ago by 3.2k
45
votes
3
replies
13k
views
Tutorial: A Wet-Lab Guide to 'what I wish I had known' for Computational Biology
bioinformatics computational-biology
updated 12 months ago by 43k • written 8.1 years ago by ★ 3.2k
1
vote
3
replies
953
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
13 months ago by barslmn ★ 2.1k
19
votes
3
replies
14k
views
Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 21 months ago by 43k • written 8.2 years ago by ★ 9.4k
2
votes
3
replies
281
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 9 hours ago by 43k • written 2 days ago by ★ 3.9k
10
votes
3
replies
4.5k
views
Tutorial: Video: Alternative Splicing and Primer Design
RNA-Seq IGB
updated 15 months ago by 43k • written 9.6 years ago by ▴ 860
51
votes
3
replies
23k
views
Tutorial: Sam File Format - Lesser Known Tips And Tricks
sam
updated 14 months ago by 43k • written 11.3 years ago by ▴ 300
0
votes
3
replies
2.5k
views
Tutorial: Automatic Primer Design
Assembly sequence
updated 20 months ago by 43k • written 8.5 years ago by ▴ 40
3
votes
3
replies
1.1k
views
Tutorial: multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation RNAseq multiomics
updated 3 months ago by ▴ 40 • written 8 months ago by ★ 3.9k
2
votes
3
replies
2.0k
views
Tutorial: Help demonstrate reproducibility in bioinformatics with the GA4GH's tool execution Challenge
GA4GH Docker CWL Rabix
updated 12 months ago by 43k • written 7.2 years ago by ▴ 20
18
votes
2
replies
10.0k
views
Tutorial: Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq Galaxy IGB
updated 2.1 years ago by 43k • written 9.5 years ago by ▴ 860
7
votes
2
replies
1.9k
views
Tutorial: Introduction to Human Genomics for Clinical Informaticists
genome
updated 11 months ago by 43k • written 6.7 years ago by ▴ 90
20
votes
2
replies
8.1k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 11 months ago by 43k • written 6.4 years ago by ★ 3.4k
22
votes
2
replies
6.0k
views
Tutorial: Use a workflow management tool to manage your computational pipelines
workflow-management snakemake pipeline
updated 12 months ago by 43k • written 7.5 years ago by ★ 2.1k
20
votes
2
replies
3.4k
views
Tutorial: Beginner's Handbook to Next Generation Sequencing
NGS
updated 11 months ago by 43k • written 7.1 years ago by ▴ 650
6
votes
2
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5.0k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
4 months ago by GenoMax 141k
8
votes
2
replies
1.1k
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 8 months ago by 43k • written 8 months ago by ★ 2.5k
60
votes
2
replies
7.4k
views
Tutorial: Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 14 months ago by 43k • written 11.7 years ago by 100k
5
votes
2
replies
2.3k
views
Tutorial: Using Bedtools Closest (closestBed) to make distance histograms of protein binding frequency near all types of pre-RNA junctions (e.g. exon-intron an…
preRNA closestBed bedtools-closest bedtools
updated 13 months ago by 43k • written 5.3 years ago by ▴ 10
8
votes
2
replies
6.6k
views
Tutorial: Troubleshooting issues with SURPI pipeline for pathogen identification from complex metagenomic NGS data.
metagenomics clinical-genomics
updated 2.2 years ago by 43k • written 9.5 years ago by 12k
4
votes
2
replies
7.2k
views
Tutorial: Analyzing Genomewide Association Study Data: A Tutorial Using Plink
plink gwas
updated 14 months ago by 43k • written 11.9 years ago by 100k
45
votes
2
replies
37k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 14 months ago by 43k • written 12.1 years ago by ▴ 540
1
vote
2
replies
3.3k
views
Tutorial: Standalone BLAST error: UnexpectedTagClassByte
software-error blast
updated 18 months ago by 43k • written 8.7 years ago by ▴ 10
3
votes
2
replies
2.9k
views
Tutorial: Running fastq_screen on your data
fastqscreen
2.1 years ago by rohitsatyam102 ▴ 850
22
votes
2
replies
5.8k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 19 months ago by ▴ 40 • written 3.0 years ago by 8.5k
5
votes
2
replies
1.7k
views
Tutorial: ENCODE 2016: Research Applications and Users Meeting
ChIP-Seq next-gen ENCODE
updated 12 months ago by 43k • written 7.9 years ago by ★ 1.1k
1
vote
2
replies
1.5k
views
Tutorial: ViennaRNA package installation in Windows
windows rna mfold viennarna
updated 10 months ago by 43k • written 19 months ago by ▴ 20
1
vote
2
replies
876
views
Tutorial: How to ask computational biology questions
computational-biology
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
15
votes
2
replies
2.1k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 18 months ago by ▴ 830 • written 2.6 years ago by ▴ 310
10
votes
2
replies
3.7k
views
Tutorial: Graph visualization with igraph in R
Visualization igraph Graph R Network
updated 11 months ago by 43k • written 7.0 years ago by 27k
4
votes
2
replies
2.5k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 13 months ago by 43k • written 4.9 years ago by ★ 9.4k
7
votes
2
replies
1.7k
views
Tutorial: A tale of two heatmap function
clustering heatmap
updated 12 months ago by 43k • written 7.6 years ago by ★ 3.9k
6
votes
2
replies
4.2k
views
Tutorial: GATK method for filtering vcf lines using GT values at all or multisample level.
genome vcf genotype variant-filtration
updated 11 months ago by 43k • written 6.9 years ago by ★ 1.6k
4
votes
2
replies
2.9k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 7 months ago by 141k • written 4.0 years ago by 82k
6
votes
2
replies
1.6k
views
Tutorial: GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma GPL6955 Microarray miRNA Agilent
2.7 years ago by Kevin Blighe 87k
15
votes
2
replies
3.0k
views
Tutorial: Introduction to bedtools.
bedtools
updated 13 months ago by 43k • written 9.4 years ago by 12k
87
votes
2
replies
59k
views
6 follow
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 14 months ago by 43k • written 10.8 years ago by 11k
411 results • Page 4 of 9
Recent Votes
A: Blast Settings For Short Sequences
A: Blast Settings For Short Sequences
Comment: Heatmap and rna-seq
Answer: Heatmap and rna-seq
Comment: Heatmap and rna-seq
A: should FASTA files be sorted before indexed with SAMtools?
Answer: A faidx-indexed FASTA format file or a FASTA format file
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Scholar to Alex Reynolds 35k
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Recent Replies
Answer: Limma Analysis Agilent Microarray Data (GPL1708) by Gordon Smyth ★ 7.0k
There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler. I don't recommend col…
Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR? by Gordon Smyth ★ 7.0k
The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1. Have you exam…
Answer: How to use limma to find differentially expressed genes in response to a continu by Gordon Smyth ★ 7.0k
There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J ▴ 10
Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J ▴ 10
Thank you Pierre! I'll try this out with my full data set.
Answer: DNA methylation preprocessing by cao510927 ▴ 30
I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
Answer: Create a new bed file with all pairwise combinations between two other bed files by Alex Reynolds 35k
I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
Comment: Highest variable features in single cell data by bk11 ★ 2.4k
You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
Comment: Heatmap and rna-seq by GenoMax 141k
Please include a link when you are recommending a tool. There can be programs with similar names.
Answer: Heatmap and rna-seq by dsull ★ 5.8k
Check out clustergrammer from Avi Ma'ayan's lab.
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by Ram 43k
Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i by ATpoint 82k
You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by BioinfGuru ★ 1.7k
Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
Comment: Low mapping rate with Salmon by i.sudbery 19k
Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
Comment: How to convert plink files to Hapmap Format by bk11 ★ 2.4k
If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value. https://www.b…
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