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323 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 9 days ago by 39k • written 7.8 years ago by ★ 4.6k
130
votes
123
replies
30k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 10 weeks ago by ★ 1.1k • written 4.6 years ago by 85k
92
votes
105
replies
36k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 11 weeks ago by 39k • written 4.8 years ago by 85k
76
votes
70
replies
16k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 11 weeks ago by 39k • written 5.3 years ago by 85k
146
votes
69
replies
44k
views
19 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 8 weeks ago by ▴ 10 • written 5.5 years ago by 85k
116
votes
66
replies
41k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 11 weeks ago by 39k • written 4.9 years ago by 72k
72
votes
60
replies
24k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 3 months ago by 39k • written 5.7 years ago by 85k
60
votes
52
replies
40k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 11 weeks ago by 39k • written 6.7 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 3 months ago by 39k • written 10.3 years ago by 33k
196
votes
44
replies
69k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 4 months ago by 39k • written 10.7 years ago by 20k
59
votes
43
replies
18k
views
18 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign pacbio arrow smrt-limk
updated 11 weeks ago by 39k • written 5.7 years ago by ★ 1.4k
78
votes
42
replies
29k
views
25 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 25 days ago by 39k • written 9.6 years ago by ★ 7.7k
18
votes
40
replies
16k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 11 weeks ago by 39k • written 6.9 years ago by ▴ 170
277
votes
39
replies
168k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 10 weeks ago by 39k • written 8.8 years ago by 20k
148
votes
35
replies
59k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 3 months ago by 39k • written 10.5 years ago by ★ 1.6k
83
votes
34
replies
16k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 7 days ago by • 0 • written 4.9 years ago by ★ 1.3k
145
votes
34
replies
52k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 3 months ago by 39k • written 10.1 years ago by 5.9k
277
votes
33
replies
94k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 3 months ago by 39k • written 9.6 years ago by 20k
12
votes
31
replies
5.1k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 12 weeks ago by 39k • written 3.8 years ago by 7.9k
82
votes
28
replies
28k
views
19 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 3 months ago by 39k • written 7.2 years ago by 20k
45
votes
28
replies
7.3k
views
9 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
15 days ago by Ram 39k
65
votes
26
replies
11k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 11 weeks ago by 39k • written 4.2 years ago by 16k
70
votes
26
replies
25k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 3 months ago by 39k • written 9.3 years ago by 98k
64
votes
26
replies
12k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 11 weeks ago by 39k • written 5.7 years ago by 85k
58
votes
25
replies
37k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 11 weeks ago by 39k • written 6.8 years ago by ★ 9.3k
94
votes
25
replies
31k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 3 months ago by 39k • written 10.7 years ago by 98k
9
votes
23
replies
8.6k
views
7 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 15 days ago by 39k • written 5.4 years ago by ▴ 310
18
votes
22
replies
7.5k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 11 weeks ago by 39k • written 3.5 years ago by 7.9k
83
votes
21
replies
16k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 12 weeks ago by 39k • written 2.6 years ago by 2.9k
82
votes
21
replies
74k
views
13 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 3 months ago by ★ 3.0k • written 4.9 years ago by ▴ 540
12
votes
20
replies
12k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 11 weeks ago by 39k • written 4.0 years ago by ★ 14k
89
votes
19
replies
31k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray bioconductor expression classification
updated 3 months ago by 39k • written 9.6 years ago by 20k
47
votes
19
replies
12k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control fastqc
updated 4 months ago by 39k • written 10.3 years ago by 98k
42
votes
19
replies
7.2k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 3 months ago by 39k • written 10.3 years ago by 4.1k
23
votes
19
replies
5.8k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
fastq mutation cancer target
updated 8 weeks ago by 39k • written 6.7 years ago by ★ 2.4k
8
votes
19
replies
12k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
mysql orthomcl
updated 12 weeks ago by 39k • written 8.5 years ago by ▴ 580
51
votes
19
replies
42k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization bigwig chip-seq rna-seq
updated 3 months ago by 39k • written 11.1 years ago by 11k
12
votes
17
replies
2.3k
views
Tutorial: How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola bwa
updated 5 months ago by 39k • written 8.0 years ago by 98k
26
votes
17
replies
6.8k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv
updated 8 months ago by 39k • written 8.8 years ago by 5.9k
8
votes
17
replies
2.4k
views
Tutorial: Simple approach to RNA-seq (T-Bioinfo platform)
alignment next-gen-sequencing RNA-seq
updated 9 months ago by 39k • written 7.6 years ago by ▴ 340
34
votes
17
replies
15k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 29 days ago by 129k • written 9.5 years ago by 20k
99
votes
16
replies
30k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 11 weeks ago by 39k • written 6.8 years ago by 26k
42
votes
16
replies
21k
views
15 follow
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC varscan2 CNV copy-number
updated 9 months ago by 39k • written 7.7 years ago by ★ 2.3k
59
votes
15
replies
12k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 8 days ago by 39k • written 4.6 years ago by 16k
34
votes
15
replies
5.3k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 11 weeks ago by 39k • written 4.0 years ago by ★ 9.3k
34
votes
15
replies
18k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 11 weeks ago by 39k • written 6.7 years ago by ▴ 310
24
votes
15
replies
8.1k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
course training mooc
updated 3 months ago by 39k • written 10.4 years ago by 9.6k
20
votes
14
replies
3.4k
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 8 weeks ago by 39k • written 7.1 years ago by ▴ 460
73
votes
14
replies
14k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 3 months ago by 39k • written 10.0 years ago by 9.6k
7
votes
14
replies
2.4k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 7 months ago by • 0 • written 15 months ago by ▴ 30
323 results • Page 1 of 7
Recent Votes
Comment: Low mapping percentage
Comment: Low mapping percentage
A: genomicranges outside sequence bounds
A: how can i download human ribosomal reference ?
Bayesian network for biological data using bnlearn
Comment: What does canonical transcript mean in the context of VEP
Answer: What does canonical transcript mean in the context of VEP
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Recent Replies
Comment: Low mapping percentage by Sib ▴ 40
Thank you for the reply. If there is not much I can do about the contamination at this stage, what is the benefit of knowing the source of…
Answer: integrate single cell RNA sequencing data by Hamid Ghaedi 2.9k
There are different approaches that you may choose to deal with batch correction. Harmony is one of those approaches that has been shown to…
Comment: What does canonical transcript mean in the context of VEP by Vincent Laufer ★ 2.9k
@curious - The only thing I have to add to @yokofakun 's precise answer is that, while you are considering and reading about Ensembl canoni…
Comment: Help with running ATAC using Encode pipeline by Chris ▴ 100
Thank you for the instruction! I see the beside json file we also have input file which I am confused. Because we have already defined the …
Comment: Comparing loci across catalogs by rycro_c • 0
Hi @Austin, Did you ever figure this out?
Comment: Low mapping percentage by Dave Carlson ★ 1.3k
I've been faced with similar issues in the past. Both option 1 and 2 seem useful. You can also treat your data as accidental metagenomic …
Comment: How to sort gff3 according to chromosome order? by Pierre Lindenbaum 154k
-s, --stable stabilize sort by disabling last-resort comparison
Comment: Low mapping percentage by GenoMax 129k
If you do have contamination (either from rRNA of same species or from true contaminant(s)) there is not much you can do about that at this…
Comment: Optimum setting for local blastp for ~10K sequences by GenoMax 129k
> Running the same sequence on the blast web server took 10 seconds Don't try to compare anything local with NCBI's web blast infrastruct…
Comment: how to Construct a Newick tree file from five large fasta files by Joe 21k
Yes, I know - but that doesn't answer the question. **What *kind* of phylogenetic tree?**
Comment: Optimum setting for local blastp for ~10K sequences by sodiumnitrate ▴ 20
Thank you for the explanation! I managed to get diamond to work, but I'm having trouble getting it to run faster than blast. For a single t…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig by GenoMax 129k
That is the question @Vincent answer poses since it seems to correspond to something different. You can also create an issue on https://gi…
Answer: How to sort gff3 according to chromosome order? by GenoMax 129k
Please use `AGAT`: https://agat.readthedocs.io/en/latest/topological-sorting-of-gff-features.html
Comment: convert data frame with character column to data frame with integer column by atemedorri137798 • 0
dear @Basti : As you said in order to clarify my issue I edit question box with give an example. I will be grateful if you take a look at …
Comment: How to sort gff3 according to chromosome order? by Ram 39k
Those are your options with the `sort` utility - you can either keep the existing order or re-order by coordinate. If you're looking for a …
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