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318 results • Page 4 of 7
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32
votes
4
replies
7.3k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 8 months ago by 41k • written 5.1 years ago by ★ 1.6k
58
votes
25
replies
39k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 8 months ago by 41k • written 7.3 years ago by ★ 9.3k
63
votes
15
replies
13k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 6 months ago by 41k • written 5.1 years ago by 16k
3
votes
4
replies
3.5k
views
Tutorial: Gene Set Enrichment Analysis on T-BioInfo
gene RNA-Seq
updated 6 months ago by 41k • written 5.1 years ago by ▴ 340
22
votes
2
replies
5.8k
views
Tutorial: Use a workflow management tool to manage your computational pipelines
workflow-management snakemake pipeline
updated 7 months ago by 41k • written 7.1 years ago by ★ 2.1k
10
votes
4
replies
3.4k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 6 months ago by 41k • written 5.8 years ago by 86k
20
votes
4
replies
14k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix
updated 9 months ago by 41k • written 10.7 years ago by 20k
0
votes
0
replies
1.2k
views
Tutorial: In the cloud - Guide to running VerifyBamID to estimate DNA sample contamination
sequence cloud dna sequencing
updated 6 months ago by 41k • written 5.3 years ago by • 0
20
votes
2
replies
7.7k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 6 months ago by 41k • written 6.0 years ago by ★ 3.4k
2
votes
0
replies
1.3k
views
Tutorial: Principal Component Analysis (PCA ON T-BIOINFO)
RNA-Seq next-gen
updated 6 months ago by 41k • written 5.5 years ago by ▴ 340
1
vote
4
replies
3.2k
views
Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq
updated 6 months ago by 41k • written 5.6 years ago by ▴ 340
3
votes
4
replies
4.3k
views
Tutorial: gencore: a tool to reduce sequencing noises by generating consensus reads
consensus OpenGene sequencing-noise
updated 6 months ago by 41k • written 5.6 years ago by ★ 2.5k
18
votes
2
replies
5.7k
views
Tutorial: Update kraken databases
database kraken k-mer python
updated 6 months ago by 41k • written 6.6 years ago by 5.3k
2
votes
0
replies
1.5k
views
Tutorial: Webinar: Extracting research evidence from publications
text-mining ontology pubmed
updated 6 months ago by 41k • written 5.8 years ago by ▴ 60
146
votes
34
replies
53k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 9 months ago by 41k • written 10.6 years ago by 6.0k
1
vote
0
replies
2.3k
views
Tutorial: Tutorial DEAP 2.1 In DOS
deap2.1 R
updated 8 months ago by 41k • written 5.8 years ago by ▴ 10
0
votes
0
replies
3.5k
views
Tutorial: SFA (Stochastic Frontier Analysis) STATA 14
R
updated 6 months ago by 41k • written 5.8 years ago by ▴ 10
0
votes
0
replies
1.5k
views
Tutorial: PLS SEM (Partial Least Square Sructural Equation Modeling) Analysis WarpPLS 6
R
updated 6 months ago by 41k • written 5.8 years ago by ▴ 10
3
votes
0
replies
2.2k
views
Tutorial: Deep Learning for Cancer Immunotherapy
keras tensorflow
updated 6 months ago by 41k • written 5.8 years ago by 22k
0
votes
0
replies
1.5k
views
Tutorial: MWD (Mackinnon, White And Davidson) In R
R
updated 6 months ago by 41k • written 5.8 years ago by ▴ 10
0
votes
0
replies
2.1k
views
Tutorial: Transforming (Transformation) Data LN, Log, SQRT In R Commander
R
updated 6 months ago by 41k • written 5.8 years ago by ▴ 10
14
votes
2
replies
2.3k
views
Tutorial: Exploring OpenSNP - an RMarkdown report on crowdsourced genotypes and phenotypes
SNP R
updated 8 months ago by 41k • written 7.7 years ago by 22k
0
votes
0
replies
3.5k
views
Tutorial: Park Test for Heteroskedasticity In R Commander
R Park-Test
updated 6 months ago by 41k • written 5.9 years ago by ▴ 10
0
votes
0
replies
7.9k
views
Tutorial: Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R eviews
updated 6 months ago by 41k • written 5.9 years ago by ▴ 10
23
votes
19
replies
6.4k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
fastq mutation cancer target
updated 7 months ago by 41k • written 7.2 years ago by ★ 2.5k
1
vote
0
replies
1.4k
views
Tutorial: Fall 2017 Introduction to Human Genomics for Clinical Informaticists
genome
updated 6 months ago by 41k • written 5.9 years ago by ▴ 90
0
votes
1
reply
1.7k
views
Tutorial: Guide Tutorial DEAP 2.1 In Windows 7
DEAP2.1 R stata
updated 8 months ago by 41k • written 5.9 years ago by ▴ 10
0
votes
1
reply
1.8k
views
Tutorial: Nonparametric Regression STATA 15
STATA-15 Nonparametric-Regression STATA
updated 6 months ago by 41k • written 5.9 years ago by ▴ 10
3
votes
3
replies
8.4k
views
Tutorial: High Speed Downloading of SRA, SAM and Fastq Files
fastq sam Aspera-Connect sra
updated 6 months ago by 41k • written 5.9 years ago by ▴ 100
2
votes
0
replies
6.7k
views
Tutorial: How to - Install Python packages in a virtual environment (virtualenv)
ubuntu cutadapt virtualenv python windows
updated 6 months ago by 41k • written 6.0 years ago by ▴ 320
0
votes
0
replies
2.8k
views
Tutorial: Autocorrelation With Breusch Godfrey Serial Correlation LM Test R Commander
LM-Test R Autocorrelation Breusch-Godfrey
updated 6 months ago by 41k • written 6.0 years ago by ▴ 10
0
votes
0
replies
3.0k
views
Tutorial: Normality Test For JB (Jarque Bera) Test R Commander
Jarque-Bera-Test R-Commander
updated 6 months ago by 41k • written 6.0 years ago by ▴ 10
0
votes
0
replies
1.3k
views
Tutorial: Data Panel In R Commander
R
updated 6 months ago by 41k • written 6.0 years ago by ▴ 10
10
votes
1
reply
8.6k
views
Tutorial: How to select reads with specific flag using samtools
next-gen-sequencing
updated 6 months ago by 41k • written 6.2 years ago by ▴ 110
1
vote
0
replies
2.0k
views
Tutorial: How to display Agilent CGH array in IGV
IGV CGH
updated 6 months ago by 41k • written 6.0 years ago by ★ 2.4k
3
votes
2
replies
8.4k
views
Tutorial: Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ UMI fastp
updated 6 months ago by 41k • written 6.0 years ago by ★ 2.5k
39
votes
6
replies
18k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
ggplot2 R chromosome karyotype
updated 6 months ago by 41k • written 6.3 years ago by ★ 3.4k
15
votes
1
reply
6.8k
views
Tutorial: A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl SAM blast BED
updated 6 months ago by 41k • written 6.0 years ago by ★ 3.0k
5
votes
5
replies
6.7k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq
updated 6 months ago by 41k • written 6.1 years ago by ▴ 130
7
votes
1
reply
2.2k
views
Tutorial: A gentle introduction to biogo
sequence golang biogo
updated 6 months ago by 41k • written 6.1 years ago by ★ 1.7k
0
votes
1
reply
3.0k
views
Tutorial: Accessing sequences using batch entrez
genome
updated 6 months ago by 41k • written 6.1 years ago by • 0
2
votes
0
replies
3.1k
views
Tutorial: use the tool slicer to split big files (like FASTQ) to smaller files for parallel processing
opengene slicer fastq splitter
updated 5 months ago by 41k • written 6.1 years ago by ★ 2.5k
5
votes
2
replies
3.0k
views
Tutorial: Get GC Content from UCSC with perl script (mysql)
myql ucsc gc-content perl
updated 6 months ago by 41k • written 6.6 years ago by ★ 9.3k
5
votes
0
replies
2.1k
views
Tutorial: Installing multiprocessor-capable MEME to work with a Slurm job scheduler environment
slurm meme parallel
updated 6 months ago by 41k • written 6.2 years ago by 35k
9
votes
9
replies
4.0k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
reference-coverage ngs
updated 6 months ago by 41k • written 6.2 years ago by 86k
12
votes
4
replies
2.0k
views
Tutorial: Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR DESeq2
updated 8 months ago by 41k • written 6.2 years ago by ▴ 590
11
votes
7
replies
14k
views
Tutorial: Removing rows with duplicate values based on 1 or more key values - linux awk
awk linux bash
updated 6 months ago by 41k • written 6.2 years ago by 86k
7
votes
2
replies
1.8k
views
Tutorial: Introduction to Human Genomics for Clinical Informaticists
genome
updated 6 months ago by 41k • written 6.3 years ago by ▴ 90
4
votes
1
reply
1.8k
views
Tutorial: One of the easy way to achieve read count and RPKM file
RNA-Seq
updated 6 months ago by 41k • written 6.3 years ago by ▴ 40
1
vote
0
replies
1.6k
views
Tutorial: Using Subversion to update /devel branch of Bioconductor package
bioconductor subversion
updated 6 months ago by 41k • written 6.3 years ago by ▴ 350
318 results • Page 4 of 7
Recent Votes
Answer: GO categorization
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
Answer: GO categorization
C: Expected a file with 2 fields per line. GenomicsDBImport from GATK ?
C: Expected a file with 2 fields per line. GenomicsDBImport from GATK ?
Answer: Problematic fastq files...How can we trust them?
Comment: Problematic fastq files...How can we trust them?
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Popular Question to beausoleilmo ▴ 560
Commentator to Brian Bushnell 19k
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Recent Replies
Comment: Should I scale all genes in single cell Seurat? by synat.keam ▴ 80
Thanks, António for your kind and detailed responses. You helped clear my doubt about scaling! Kind Regards, Synat
Comment: Using metagenome assembly and binning to identify and mitigate contamination in by Brian Bushnell 19k
It's not a silly question! And yes, it can be done. JGI is currently testing various binning tools to try to find the best protocol for t…
Answer: GO categorization by geneontologyhelp ▴ 270
[We have this in our FAQ][1]. PANTHER version 18.0, which powers the enrichment analysis on our homepage, has [143 species][2] loaded and …
Comment: Problematic fastq files...How can we trust them? by blackadder ▴ 30
Thanks for the feedback fellas! I agree with the aforementioned!
Comment: Which program, tool, or strategy do you use to visualize genomic rearrangements? by cmdcolin ★ 3.4k
i collect a large list of tools for visualization, some are specialized for SVs and re-arrangements. you can filter by tag (SV, CNV, compar…
Answer: The number of variations in the pan-genome is reduced compared to the variations by Jordan M Eizenga ▴ 410
If variants overlap in the genome, `vg deconstruct` will combine them into one locus with multiple alleles. If your input VCF has a lot of …
Answer: How to find node Postion and source(sample) ? by Jordan M Eizenga ▴ 410
You can use `vg find -P` for this. This command is not really designed to be used frequently throughout the genome (each invocation loads t…
Comment: How Can I move the scattered dots more closer into the center of box ? by Brian Bushnell 19k
I would just draw them in by hand where you want them.
Comment: How to identify CG, CHG, or CHH from MeDIP data by Tm ★ 1.1k
I know that CpG types can be identified using whole genome bisulphite data. But could it be possible using MeDIP data too? We tried using Q…
Comment: Problematic fastq files...How can we trust them? by Brian Bushnell 19k
I'd have to agree there... while you can generally recover a fastq to the point that it is spec-compliant, you don't know how or why the f…
Answer: Finding human .vcf files online to download by cmdcolin ★ 3.4k
---------- some common ones include 1000 genomes vcf (large, multi-sample) http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ …
Comment: GO categorization by m.habib • 0
Thanks Istvan for your reply. I think these programs will do the same as Trinotate. Trinotate searches against numerous databases and gener…
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by jv ★ 1.2k
I wonder if using cell hashing, which would allow pooling of cells from multiple samples before droplet formation, could improve things her…
Comment: Where Can I Find The Basepair Positions Of Chromosome Bands? by Malachi Griffith 19k
And the hg38 version can be found here: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz And for convenience, upda…
Answer: How Can I move the scattered dots more closer into the center of box ? by Trivas ★ 1.5k
You added a position dodge on your boxplot but not on your points.
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