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Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 3 months ago by 40k • written 8.1 years ago by ★ 4.7k
132
votes
123
replies
32k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 6 months ago by ★ 1.1k • written 4.9 years ago by 86k
93
votes
105
replies
39k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 6 months ago by 40k • written 5.1 years ago by 86k
146
votes
70
replies
46k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 23 days ago by ▴ 260 • written 5.8 years ago by 86k
76
votes
70
replies
17k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 6 months ago by 40k • written 5.6 years ago by 86k
116
votes
66
replies
43k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 6 months ago by 40k • written 5.2 years ago by 76k
73
votes
60
replies
25k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 7 months ago by 40k • written 6.0 years ago by 86k
60
votes
52
replies
41k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 6 months ago by 40k • written 7.0 years ago by ★ 3.3k
72
votes
48
replies
16k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs alignment bwa
updated 6 months ago by 40k • written 10.6 years ago by 33k
196
votes
44
replies
69k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 8 months ago by 40k • written 11.0 years ago by 20k
59
votes
43
replies
19k
views
18 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign pacbio arrow smrt-limk
updated 6 months ago by 40k • written 6.0 years ago by ★ 1.4k
82
votes
43
replies
30k
views
26 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 12 weeks ago by ▴ 40 • written 9.9 years ago by ★ 7.7k
18
votes
40
replies
17k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 6 months ago by 40k • written 7.2 years ago by ▴ 170
282
votes
39
replies
173k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 6 months ago by 40k • written 9.1 years ago by 20k
149
votes
35
replies
60k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 6 months ago by 40k • written 10.8 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 3 months ago by • 0 • written 5.2 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 6 months ago by 40k • written 10.4 years ago by 6.0k
288
votes
33
replies
99k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 6 months ago by 40k • written 9.9 years ago by 20k
13
votes
31
replies
5.7k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 6 months ago by 40k • written 4.1 years ago by 8.2k
84
votes
29
replies
30k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 8 weeks ago by • 0 • written 7.5 years ago by 20k
48
votes
28
replies
8.5k
views
9 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
4 months ago by Ram 40k
64
votes
26
replies
12k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 6 months ago by 40k • written 6.0 years ago by 86k
65
votes
26
replies
13k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 6 months ago by 40k • written 4.5 years ago by 16k
71
votes
26
replies
26k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 6 months ago by 40k • written 9.6 years ago by 98k
58
votes
25
replies
38k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 6 months ago by 40k • written 7.2 years ago by ★ 9.3k
137
votes
25
replies
79k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 17 months ago by 40k • written 11.4 years ago by ★ 4.2k
95
votes
25
replies
32k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 7 months ago by 40k • written 11.0 years ago by 98k
9
votes
23
replies
9.1k
views
7 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 4 months ago by 40k • written 5.7 years ago by ▴ 310
18
votes
22
replies
8.0k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 6 months ago by 40k • written 3.8 years ago by 8.2k
86
votes
22
replies
80k
views
14 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 10 weeks ago by • 0 • written 5.2 years ago by ▴ 580
84
votes
21
replies
18k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 6 months ago by 40k • written 2.9 years ago by 3.0k
142
votes
21
replies
29k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 16 months ago by 40k • written 8.8 years ago by ★ 1.6k
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 6 months ago by 40k • written 4.3 years ago by ★ 15k
53
votes
19
replies
42k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization bigwig chip-seq rna-seq
updated 7 months ago by 40k • written 11.4 years ago by 11k
8
votes
19
replies
12k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
mysql orthomcl
updated 6 months ago by 40k • written 8.8 years ago by ▴ 590
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 6 months ago by 40k • written 9.9 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 8 months ago by 40k • written 10.6 years ago by 98k
42
votes
19
replies
7.4k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 6 months ago by 40k • written 10.6 years ago by 4.1k
23
votes
19
replies
6.1k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
fastq mutation cancer target
updated 5 months ago by 40k • written 7.0 years ago by ★ 2.4k
26
votes
17
replies
7.1k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv
updated 12 months ago by 40k • written 9.1 years ago by 6.0k
12
votes
17
replies
2.5k
views
Tutorial: How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola bwa
updated 9 months ago by 40k • written 8.3 years ago by 98k
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 4 months ago by 134k • written 9.8 years ago by 20k
8
votes
17
replies
2.7k
views
Tutorial: Simple approach to RNA-seq (T-Bioinfo platform)
alignment next-gen-sequencing RNA-seq
updated 12 months ago by 40k • written 7.9 years ago by ▴ 340
99
votes
16
replies
31k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 6 months ago by 40k • written 7.1 years ago by 26k
42
votes
16
replies
22k
views
15 follow
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC varscan2 CNV copy-number
updated 13 months ago by 40k • written 8.0 years ago by ★ 2.4k
34
votes
15
replies
19k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 6 months ago by 40k • written 7.0 years ago by ▴ 310
61
votes
15
replies
13k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 3 months ago by 40k • written 4.9 years ago by 16k
34
votes
15
replies
5.8k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 6 months ago by 40k • written 4.3 years ago by ★ 9.3k
25
votes
15
replies
8.4k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
course training mooc
updated 6 months ago by 40k • written 10.7 years ago by 9.7k
20
votes
14
replies
3.6k
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 5 months ago by 40k • written 7.4 years ago by ▴ 460
379 results • Page 1 of 8
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What is the difference between norm --multiallelics -any versus --atomize?
Answer: What is the difference between norm --multiallelics -any versus --atomize?
A: How To Extract A Sequence From A Big (6Gb) Multifasta File ?
A: How to extract a sequence below a fasta header (">") from a fasta file ?
A: How to extract a sequence below a fasta header (">") from a fasta file ?
A: How To Extract A Sequence From A Big (6Gb) Multifasta File ?
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Answer: How to find positions with higher depth relative to their surroundings by xiaoguang ▴ 120
I saw you want to get regions that have significantly higher depth than their surroundings; you must get a p-value to show significant as w…
Comment: how to calculate BAF and LRR from VCF or BCF files? by xiaoguang ▴ 120
Hi, The ASCAT new version has introduced a new function called `ascat.prepareHTS`, which can be used to prepare all files that are required…
Comment: GERP++ (gerpcol) error on a test data by Diana • 0
I solved the problem in the end. I was under the impression that the reference sequence had to be provided in a separate fasta file: c…
Answer: How to find positions with higher depth relative to their surroundings by d-cameron ★ 2.9k
The usual way of doing this is to use one of the many existing copy number variant caller. Doing this yourself is both a) complicated to do…
Answer: How to retrieve LoF and missense variants in WES data? by luffy ▴ 30
@ _quantum_girl_, as Pierre mentioned, you can annotate your VCF with [snpEff][1] or [ensembl vep][2] once you annotated you could filter n…
Comment: Adding a control sample to bulk RNA-seq by Chris ▴ 180
Thank you so much! It is from the same lab but from another project. Would you please explain about combining the counts together a little …
Answer: Importance of Data Structures for Bioinformatics? by d-cameron ★ 2.9k
> how important are Data Structures to multi-omic / bioinformatic analysis Generally speaking, they're not critical if you are using an …
Answer: Recommended order of operations for identifying the genomic location and copy-nu by dk0319 ▴ 70
Update: The above workflow was successful, in that contig_1719 does contain approximately 4 copies of my insert based on searching pieces o…
Comment: manhattan plot with vcf information by sooni ▴ 10
I want to find out specific genes using the manhattan plot. I divide the patients into two groups, controls and patients, and try to identi…
Comment: Importance of Data Structures for Bioinformatics? by dsull ★ 4.6k
If you don't want to hurt your GPA, why not just take the course pass/fail or, if that's not an option, simply audit it? I doubt anyone wi…
Comment: How to DESeq2 using miRNA data obtained using TCGAbiolinks by swbarnes2 13k
miRNAs are rather small, and your typical RNASeq library prep will remove small sequences. Are you sure that the data you are trying to ge…
Comment: Inflated GWAS test statistic after merging multiple batches of genotype dataset by LauferVA 3.7k
even these measures will very often not fix the problem in the context of a problem of a problem of perfect separation such as OP describes.
Comment: Inflated GWAS test statistic after merging multiple batches of genotype dataset by LauferVA 3.7k
Hi Amy, I understand, this is why I said, > "The degree to which this is possible depends on the relative content > of each study - e.g. …
Answer: What is the difference between norm --multiallelics -any versus --atomize? by Ram 40k
I don't think atomization compares to norm with respect to multiallelic sites. You can see an example of atomatization on a multi-allelic s…
Comment: How to display all top markers in the heatmap by DoHeatmap (Seurat) when there a by alwayshope ▴ 30
Great guidance! Thank you very much!
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