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412 results • Page 6 of 9
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Tutorial: How to extract and filter SNP data from the genotyping-by-sequencing (GBS) data in vcf format using bcftools
bcftools SNP-Filtering VCF
updated 14 months ago by 43k • written 4.2 years ago by ▴ 10
8
votes
1
reply
1.9k
views
Tutorial: A Guide to DNA Sequencing Techniques Part 1
dna sanger sequencing pyrosequencing
updated 14 months ago by 43k • written 8.8 years ago by ▴ 430
4
votes
1
reply
6.1k
views
Tutorial: Chip-Seq Data Analysis Tutorial
chip-seq
updated 15 months ago by 43k • written 12.0 years ago by ▴ 360
0
votes
1
reply
3.0k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
biosql python taxonomy
updated 14 months ago by 43k • written 5.8 years ago by ▴ 320
8
votes
1
reply
1.4k
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
fasta awk
updated 14 months ago by 43k • written 3.2 years ago by 88k
0
votes
1
reply
1.8k
views
Tutorial: Guide Tutorial DEAP 2.1 In Windows 7
DEAP2.1 R stata
updated 14 months ago by 43k • written 6.4 years ago by ▴ 10
15
votes
1
reply
7.2k
views
Tutorial: A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl SAM blast BED
updated 12 months ago by 43k • written 6.5 years ago by ★ 3.0k
6
votes
1
reply
7.8k
views
Tutorial: Expression Analysis Of Rna-Seq Experiments With Tophat And Cufflinks
tophat RNA-seq cufflinks
updated 15 months ago by 43k • written 12.0 years ago by 100k
6
votes
1
reply
3.0k
views
Tutorial: Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
ChIP-Seq peak-calling sequencing
updated 14 months ago by 43k • written 10.1 years ago by ▴ 220
7
votes
1
reply
196
views
Tutorial: removeBatchEffect explained using base R linear models
limma effects batch removebatcheffects
updated 10 days ago by 14k • written 10 days ago by ▴ 360
1
vote
1
reply
1.8k
views
Tutorial: Live webinar: Implications of Next Generation Sequencing in Molecular Diagnosis of Cancer on 28 Sep 2016
alignment sequencing genome SNP
updated 13 months ago by 43k • written 7.7 years ago by ▴ 70
12
votes
1
reply
5.1k
views
Tutorial: RepSeq data processing and analysis
immunology tcr repseq sequencing repertoire
updated 19 months ago by 43k • written 8.8 years ago by 3.5k
10
votes
1
reply
9.3k
views
Tutorial: How to select reads with specific flag using samtools
next-gen-sequencing
updated 12 months ago by 43k • written 6.7 years ago by ▴ 110
0
votes
1
reply
2.2k
views
Tutorial: From Genefiltering to Results storgae in Microarray Analysis using in R (Part II) - FARMS
gene R
updated 13 months ago by 43k • written 7.9 years ago by ▴ 140
7
votes
1
reply
2.3k
views
Tutorial: A gentle introduction to biogo
sequence golang biogo
updated 12 months ago by 43k • written 6.6 years ago by ★ 1.7k
6
votes
1
reply
2.6k
views
Tutorial: Nice simple interactive Vim tutorial
vim linux
updated 14 months ago by 43k • written 9.5 years ago by 9.7k
0
votes
1
reply
2.7k
views
Tutorial: Clustering and results Display from PART II (PART III) - MeV software version
gene R
updated 13 months ago by 43k • written 7.9 years ago by ▴ 140
14
votes
1
reply
3.1k
views
Tutorial: PCR Primer or Primer+Probe design
pcr probe rt-pcr qpcr primer
updated 2.9 years ago by ★ 16k • written 3.0 years ago by 88k
4
votes
1
reply
1.4k
views
Tutorial: Real World BEDtools. Practical Examples for Variant Filtering and Gene Annotations
BED BEDtools
updated 14 months ago by 43k • written 3.8 years ago by ▴ 40
50
votes
1
reply
8.9k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 15 months ago by 43k • written 3.7 years ago by 82k
2
votes
1
reply
477
views
Tutorial: Single-cell RNA-seq: Preprocessing: Clustering space and evaluation
scRNA-seq space clustering
updated 4 months ago by 43k • written 4 months ago by ▴ 120
2
votes
1
reply
1.6k
views
Tutorial: A very simple way to detect viruses and microorganisms from mNGS FASTQ data using fastv
SARS-CoV-2 fastv COVID-19 viruses
updated 14 months ago by 43k • written 4.0 years ago by ★ 2.5k
10
votes
1
reply
2.3k
views
Tutorial: introduce a tool for fast identification of SARS-CoV-2 and other microbes from sequencing data
SARS-CoV-2 fastv COVID-19
updated 14 months ago by 43k • written 4.1 years ago by ★ 2.5k
0
votes
0
replies
695
views
Tutorial: T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq TCR single-cell computational biology
9 months ago by Ming Tommy Tang ★ 3.9k
7
votes
0
replies
3.0k
views
Tutorial: On the concept of constant or intercept used in Differential Expression (DE) analysis
regression limma DESeq2
updated 13 months ago by 43k • written 8.0 years ago by ★ 5.1k
0
votes
0
replies
699
views
Tutorial: How to start disease research quickly and easily?
proteins pathways disease research-design genes
11 months ago by Coremine Medical ▴ 20
0
votes
0
replies
394
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
5 months ago by rohitsatyam102 ▴ 860
4
votes
0
replies
2.3k
views
Tutorial: Accurate prediction of active enhancers using PARE
ChIP-Seq histone-modification enhancer
updated 12 months ago by 43k • written 7.1 years ago by ▴ 100
1
vote
0
replies
1.5k
views
Tutorial: Fall 2017 Introduction to Human Genomics for Clinical Informaticists
genome
updated 12 months ago by 43k • written 6.4 years ago by ▴ 90
1
vote
0
replies
2.4k
views
Tutorial: Using wgsim to generate mate pair and single reads
wgsim
updated 21 months ago by 43k • written 8.6 years ago by ▴ 430
1
vote
0
replies
559
views
Tutorial: cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
transcriptome rstats spatial single-cell
9 months ago by Ming Tommy Tang ★ 3.9k
7
votes
0
replies
613
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
9 months ago by barslmn ★ 2.2k
5
votes
0
replies
1.9k
views
Tutorial: Gatk December Workshop Presentations
gatk
updated 14 months ago by 43k • written 11.3 years ago by ★ 5.3k
9
votes
0
replies
8.7k
views
Tutorial: Installing And Running Ncbi Blast
blast
updated 15 months ago by 43k • written 12.1 years ago by ▴ 540
28
votes
0
replies
3.7k
views
Tutorial: Building Docker images
singularity docker container
22 months ago by ATpoint 82k
4
votes
0
replies
2.3k
views
Tutorial: Exploring Encode Data In The Ucsc Genome Browser
encode
updated 15 months ago by 43k • written 11.8 years ago by 11k
2
votes
0
replies
1.2k
views
Tutorial: GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo R data-mining Gene-pathway-enrichment RNA-Seq
updated 11 months ago by 43k • written 16 months ago by ▴ 420
3
votes
0
replies
2.3k
views
Tutorial: Deep Learning for Cancer Immunotherapy
keras tensorflow
updated 12 months ago by 43k • written 6.3 years ago by 22k
1
vote
0
replies
294
views
Tutorial: Bulk RNA-seq: TCGA database preprocess
RNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
replies
1.1k
views
Tutorial: BrainArray CDF, annotation, etc
db brainarray cdf
updated 14 months ago by 43k • written 3.7 years ago by 88k
0
votes
0
replies
1.1k
views
Tutorial: Introduction to Gen3 Webinar
gen3 open-source data-commons big-data
updated 14 months ago by 43k • written 5.3 years ago by ▴ 310
0
votes
0
replies
1.4k
views
Tutorial: Webinar: Accelerating skin research by pre-screening of molecules for skin sensitization risk
skin-sensitization chemoinformatics
updated 13 months ago by 43k • written 7.5 years ago by ▴ 10
0
votes
0
replies
2.1k
views
Tutorial: New GATB-Core Tutorial: learn the Genome Analysis Tool Box... online
next-gen GATB
updated 13 months ago by 43k • written 7.5 years ago by ▴ 140
6
votes
0
replies
3.2k
views
Tutorial: Uc Riverside Bioinformatics Manuals
computing-manuals
updated 15 months ago by 43k • written 12.1 years ago by 26k
2
votes
0
replies
442
views
Tutorial: Bulk RNA-seq: WGCNA (Weighted gene co-expression network analysis) analysis
WGCNA RNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
replies
1.3k
views
Tutorial: In the cloud - Guide to running VerifyBamID to estimate DNA sample contamination
sequence cloud dna sequencing
updated 11 months ago by 43k • written 5.8 years ago by • 0
0
votes
0
replies
1.5k
views
Tutorial: RAE Method for DNAcopy
R
updated 13 months ago by 43k • written 8.2 years ago by • 0
2
votes
0
replies
3.3k
views
Tutorial: use the tool slicer to split big files (like FASTQ) to smaller files for parallel processing
opengene slicer fastq splitter
updated 11 months ago by 43k • written 6.6 years ago by ★ 2.5k
6
votes
0
replies
5.7k
views
Tutorial: How to download GEO data Quickly and easily
geo RNA-Seq R data-mining
14 months ago by Novogene ▴ 420
0
votes
0
replies
347
views
Tutorial: How to convert sra files to fastq files using parallelized fastq-dump
fastq sra
3 months ago by Ming Tommy Tang ★ 3.9k
412 results • Page 6 of 9
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Recent Replies
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…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by Ram 43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs by BATMAN • 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
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