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412 results • Page 4 of 9
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19
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3
replies
14k
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Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 22 months ago by 43k • written 8.3 years ago by ★ 9.4k
7
votes
3
replies
2.6k
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
updated 13 months ago by ▴ 110 • written 21 months ago by 88k
13
votes
3
replies
5.1k
views
Tutorial: Video: Visualization of whole genome DNA methylation data in IGB
Bismark BS-Seq RNA-Seq IGB
updated 24 months ago by 43k • written 9.2 years ago by ▴ 860
16
votes
3
replies
4.7k
views
Tutorial: NCBI blast tutorial
ncbi blast
updated 13 months ago by 43k • written 8.1 years ago by 11k
16
votes
3
replies
4.4k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 3.2 years ago by • 0 • written 3.6 years ago by 3.2k
6
votes
3
replies
4.5k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment sequencing RNA-seq gene
updated 14 months ago by 43k • written 5.6 years ago by ▴ 40
6
votes
3
replies
5.7k
views
Tutorial: High Throughput Sequence Analysis With R And Bioconductor
bioconductor
updated 15 months ago by 43k • written 11.9 years ago by 100k
2
votes
3
replies
2.7k
views
Tutorial: It's about the journey, and not the destination
R network
updated 12 months ago by 43k • written 7.1 years ago by ★ 1.2k
1
vote
3
replies
3.3k
views
Tutorial: resolving error of sspace_standard
software-error Assembly
updated 13 months ago by 43k • written 7.7 years ago by ▴ 300
0
votes
3
replies
53k
views
Tutorial: Installation VMD on LINUX_64
gromacs VMD
updated 13 months ago by 43k • written 7.9 years ago by ▴ 10
3
votes
3
replies
2.9k
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC TCGABiolinks STAR
updated 15 months ago by 43k • written 2.1 years ago by ★ 4.3k
1
vote
3
replies
975
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
13 months ago by barslmn ★ 2.2k
5
votes
3
replies
4.2k
views
Tutorial: Chip Seq Review Papers
chip-seq
updated 14 months ago by 43k • written 11.5 years ago by ▴ 80
0
votes
3
replies
2.5k
views
Tutorial: Automatic Primer Design
Assembly sequence
updated 21 months ago by 43k • written 8.5 years ago by ▴ 40
10
votes
3
replies
4.5k
views
Tutorial: Video: Alternative Splicing and Primer Design
RNA-Seq IGB
updated 16 months ago by 43k • written 9.7 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
7
votes
3
replies
3.0k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 29 days ago by 6.4k • written 16 months ago by ▴ 130
3
votes
3
replies
8.8k
views
Tutorial: High Speed Downloading of SRA, SAM and Fastq Files
fastq sam Aspera-Connect sra
updated 12 months ago by 43k • written 6.4 years ago by ▴ 100
5
votes
3
replies
5.4k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 14 months ago by • 0 • written 6.6 years ago by ▴ 140
9
votes
3
replies
4.2k
views
Tutorial: Ht Sequence Analysis With R And Bioconductor By The Bioinformatics Center At Uc Riverside
bioconductor
updated 15 months ago by 43k • written 11.7 years ago by 100k
75
votes
3
replies
39k
views
Tutorial: Revisiting the FastQC read duplication report
fastqc
updated 2.5 years ago by 43k • written 9.8 years ago by 100k
3
votes
3
replies
1.2k
views
Tutorial: multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation RNAseq multiomics
updated 4 months ago by ▴ 40 • written 8 months ago by ★ 3.9k
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 13 months ago by 43k • written 8.1 years ago by ★ 3.2k
42
votes
2
replies
18k
views
Tutorial: Sequencing Technology Review Papers
sequencing papers
updated 15 months ago by 43k • written 11.7 years ago by 100k
3
votes
2
replies
5.3k
views
Tutorial: Reorder Vcf Files
vcf
updated 14 months ago by 43k • written 11.0 years ago by ▴ 60
20
votes
2
replies
8.1k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 12 months ago by 43k • written 6.5 years ago by ★ 3.4k
20
votes
2
replies
3.4k
views
Tutorial: Beginner's Handbook to Next Generation Sequencing
NGS
updated 12 months ago by 43k • written 7.1 years ago by ▴ 650
7
votes
2
replies
3.9k
views
Tutorial: How to extract fastq files from SRA data that contains both paired and unpaired reads
fastq-dump sra
updated 13 months ago by 43k • written 8.1 years ago by ▴ 850
0
votes
2
replies
5.4k
views
Tutorial: Install AMOS on Ubuntu 13.10
sequencing alignment software-error next-gen
updated 2.5 years ago by 43k • written 9.9 years ago by 9.7k
5
votes
2
replies
3.1k
views
Tutorial: Get GC Content from UCSC with perl script (mysql)
myql ucsc gc-content perl
updated 12 months ago by 43k • written 7.1 years ago by ★ 9.4k
9
votes
2
replies
5.5k
views
Tutorial: From Data import to Normalization in Microarray Analysis using in R (Part I)
gene R
updated 13 months ago by 43k • written 7.9 years ago by ▴ 140
7
votes
2
replies
12k
views
Tutorial: Howto use NCBI programs behind a HTTP proxy
blast-plus HTTP-proxy SRA-toolkit
updated 22 months ago by 43k • written 8.3 years ago by ★ 1.8k
18
votes
2
replies
10k
views
Tutorial: Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq Galaxy IGB
updated 2.2 years ago by 43k • written 9.6 years ago by ▴ 860
0
votes
2
replies
2.4k
views
Tutorial: COURSE: NGS variant analysis and interpretation for translational research
CNIO course translational
updated 13 months ago by 43k • written 7.7 years ago by ▴ 190
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 88k
4
votes
2
replies
2.9k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 8 months ago by 142k • written 4.0 years ago by 82k
7
votes
2
replies
3.6k
views
Tutorial: List Of Tools For Mapping High-Throughput Sequencing Data (2012)
next-gen mapping
updated 14 months ago by 43k • written 11.6 years ago by 11k
45
votes
2
replies
37k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 15 months ago by 43k • written 12.1 years ago by ▴ 540
23
votes
2
replies
5.9k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 20 months ago by ▴ 40 • written 3.1 years ago by 8.6k
22
votes
2
replies
6.0k
views
Tutorial: Use a workflow management tool to manage your computational pipelines
workflow-management snakemake pipeline
updated 13 months ago by 43k • written 7.5 years ago by ★ 2.1k
15
votes
2
replies
2.1k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 19 months ago by ▴ 830 • written 2.7 years ago by ▴ 360
6
votes
2
replies
2.7k
views
Tutorial: Tutorial Bioinformatics Static Website
website
updated 14 months ago by 43k • written 10.3 years ago by ▴ 610
15
votes
2
replies
3.1k
views
Tutorial: Introduction to bedtools.
bedtools
updated 14 months ago by 43k • written 9.5 years ago by 12k
3
votes
2
replies
2.9k
views
Tutorial: Running fastq_screen on your data
fastqscreen
2.2 years ago by rohitsatyam102 ▴ 860
3
votes
2
replies
8.9k
views
Tutorial: Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ UMI fastp
updated 12 months ago by 43k • written 6.5 years ago by ★ 2.5k
6
votes
2
replies
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
5 months ago by GenoMax 142k
8
votes
2
replies
1.2k
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 9 months ago by 43k • written 9 months ago by ★ 2.5k
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 14 months ago by 43k • written 5.3 years ago by ▴ 10
7
votes
2
replies
1.7k
views
Tutorial: A tale of two heatmap function
clustering heatmap
updated 13 months ago by 43k • written 7.7 years ago by ★ 3.9k
10
votes
2
replies
3.7k
views
Tutorial: Graph visualization with igraph in R
Visualization igraph Graph R Network
updated 12 months ago by 43k • written 7.1 years ago by 27k
412 results • Page 4 of 9
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Comment: scRNAseq Differential expression analysis
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Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot by LauferVA 4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot by bk11 ★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool by ntsopoul ▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool by GenoMax 142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by bk11 ★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs by dthorbur ★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: how to treat the replicates while performing WGCNA by andres.firrincieli 3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated by alanh ▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data? by Zhenyu Zhang ★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
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