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318 results • Page 1 of 7
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Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 6 months ago by 41k • written 8.3 years ago by ★ 4.7k
132
votes
123
replies
34k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 8 months ago by ★ 1.1k • written 5.1 years ago by 86k
95
votes
105
replies
41k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 8 months ago by 41k • written 5.3 years ago by 86k
76
votes
70
replies
18k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 8 months ago by 41k • written 5.8 years ago by 86k
148
votes
70
replies
48k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 3 months ago by ▴ 260 • written 6.0 years ago by 86k
117
votes
66
replies
44k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 8 months ago by 41k • written 5.4 years ago by 78k
73
votes
60
replies
26k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 9 months ago by 41k • written 6.2 years ago by 86k
60
votes
52
replies
42k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 8 months ago by 41k • written 7.2 years ago by ★ 3.4k
90
votes
48
replies
31k
views
29 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 29 days ago by 41k • written 10.1 years ago by ★ 7.8k
72
votes
48
replies
17k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs alignment bwa
updated 9 months ago by 41k • written 10.8 years ago by 33k
196
votes
44
replies
70k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 10 months ago by 41k • written 11.2 years ago by 20k
59
votes
43
replies
20k
views
18 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign pacbio arrow smrt-limk
updated 8 months ago by 41k • written 6.2 years ago by ★ 1.4k
282
votes
39
replies
177k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 8 months ago by 41k • written 9.3 years ago by 20k
149
votes
35
replies
61k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 9 months ago by 41k • written 11.0 years ago by ★ 1.6k
83
votes
34
replies
17k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 6 months ago by • 0 • written 5.4 years ago by ★ 1.3k
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
288
votes
33
replies
102k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 9 months ago by 41k • written 10.1 years ago by 20k
14
votes
31
replies
6.1k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 8 months ago by 41k • written 4.3 years ago by 8.4k
10
votes
31
replies
10.0k
views
10 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 5 weeks ago by • 0 • written 5.9 years ago by ▴ 320
48
votes
30
replies
9.3k
views
11 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 4 weeks ago by 78k • written 7.7 years ago by 41k
84
votes
29
replies
30k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 4 months ago by • 0 • written 7.7 years ago by 20k
65
votes
26
replies
13k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 8 months ago by 41k • written 4.7 years ago by 16k
64
votes
26
replies
13k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 8 months ago by 41k • written 6.2 years ago by 86k
72
votes
26
replies
27k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 9 months ago by 41k • written 9.8 years ago by 99k
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
95
votes
25
replies
32k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 9 months ago by 41k • written 11.2 years ago by 99k
88
votes
22
replies
83k
views
14 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 4 months ago by • 0 • written 5.4 years ago by ▴ 580
18
votes
22
replies
8.4k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 10 weeks ago by ▴ 20 • written 4.0 years ago by 8.4k
84
votes
21
replies
20k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 8 months ago by 41k • written 3.1 years ago by 3.1k
12
votes
20
replies
13k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 8 months ago by 41k • written 4.5 years ago by ★ 16k
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
42
votes
19
replies
7.6k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 9 months ago by 41k • written 10.8 years ago by 4.1k
8
votes
19
replies
13k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
mysql orthomcl
updated 8 months ago by 41k • written 9.0 years ago by ▴ 600
90
votes
19
replies
31k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray bioconductor expression classification
updated 9 months ago by 41k • written 10.1 years ago by 20k
47
votes
19
replies
13k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control fastqc
updated 10 months ago by 41k • written 10.8 years ago by 99k
53
votes
19
replies
43k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization bigwig chip-seq rna-seq
updated 9 months ago by 41k • written 11.6 years ago by 11k
35
votes
17
replies
16k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 7 months ago by 136k • written 10.0 years ago by 20k
12
votes
17
replies
2.6k
views
Tutorial: How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola bwa
updated 11 months ago by 41k • written 8.5 years ago by 99k
99
votes
16
replies
32k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 8 months ago by 41k • written 7.3 years ago by 26k
25
votes
15
replies
8.6k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
course training mooc
updated 9 months ago by 41k • written 10.9 years ago by 9.7k
34
votes
15
replies
19k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 8 months ago by 41k • written 7.2 years ago by ▴ 310
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
34
votes
15
replies
6.0k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 8 months ago by 41k • written 4.5 years ago by ★ 9.3k
36
votes
14
replies
32k
views
14 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 25 days ago by ▴ 50 • written 3.3 years ago by ▴ 160
75
votes
14
replies
15k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 9 months ago by 41k • written 10.5 years ago by 9.7k
51
votes
14
replies
79k
views
10 follow
Tutorial: Using R in Conda
R
updated 8 months ago by 41k • written 3.4 years ago by ▴ 780
30
votes
14
replies
16k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 9 months ago by 41k • written 10.8 years ago by 6.0k
20
votes
14
replies
3.7k
views
Tutorial: Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data visualization and exploration (Windows)
ChIP-Seq visualization Windows EaSeq
updated 7 months ago by 41k • written 7.6 years ago by ▴ 460
4
votes
13
replies
12k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 5 months ago by 41k • written 4.8 years ago by ▴ 140
19
votes
13
replies
7.9k
views
10 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 29 days ago by • 0 • written 17 months ago by 78k
318 results • Page 1 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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Recent Awards • All
Popular Question to beausoleilmo ▴ 560
Commentator to Brian Bushnell 19k
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Recent Replies
Comment: "MethylKit" package for WGBS data by viveksomya123 • 0
Why I am getting this histogram of CpG coverage using methylkit, is this the failure of bisulfite library preparation![enter image descript…
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…
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