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318 results • Page 1 of 7
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238
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176
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90k
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73 follow
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
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
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
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
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
90
votes
48
replies
31k
views
29 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 4 weeks ago by 41k • written 10.1 years ago by ★ 7.8k
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 5.5 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
9.4k
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 7.8 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
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
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
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
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 7.4 years ago by ★ 9.3k
88
votes
22
replies
84k
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
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
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
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
23
votes
19
replies
6.4k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
fastq mutation cancer target
updated 8 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
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
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
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
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
63
votes
15
replies
13k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 6 months ago by 41k • written 5.2 years ago by 16k
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
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
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
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
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
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
36
votes
14
replies
32k
views
14 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 27 days ago by ▴ 50 • written 3.3 years ago by ▴ 160
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 8 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 4 weeks ago by • 0 • written 17 months ago by 78k
318 results • Page 1 of 7
Recent Votes
Comment: Bioinformatics: what do you think of it in the next 20 years?
Comment: KEGG DATABASE
Answer: From TPM to raw counts
Answer: GENE ONTOLOGY FOR TOMATO-ITAG4.1 OR 4
Answer: From TPM to raw counts
Comment: From TPM to raw counts
NOEL: An extremely fast Non-Overlapping Exon Length calculator written in Rust
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Answer: sequencing data from different samples in the Integrative Genome Viewer (IGV) by dunia.aburizeg ▴ 40
Check out their documentation on the official IGV website. There is also a YouTube channel for IGV that can be a good start.
Comment: Error in blast+ by Shahin • 0
Spaces are not much better in Linux either. Better never use spaces in naming files, and directories, and column names in SQL Database stru…
Comment: Which language use as a beginner in Bioinformatics and Computational genomics by rpolicastro 12k
awk is turing complete /s
Comment: sequencing data from different samples in the Integrative Genome Viewer (IGV) by rpolicastro 12k
Generally we don't provide answers for assignments here. As a *very* generic hint you can download the human reference and variants from pl…
Comment: Understanding gene level copy number data from TCGAbiolinks by bioinfo355 • 0
Were you able to get answer for your questions?
Answer: Error in blast+ by Mensur Dlakic ★ 25k
Joys of doing Bioinformatics on Windows, and consequently dealing with spaces in file and directory names. I suggest you move your datab…
Comment: Which language use as a beginner in Bioinformatics and Computational genomics by Mensur Dlakic ★ 25k
I assume here you mean the usefulness for common tasks such as file manipulation and pipeline creations. How would one do sequence assembly…
Answer: Which language use as a beginner in Bioinformatics and Computational genomics by Mensur Dlakic ★ 25k
There is no single language that is best suited for all areas of Bioinformatics. If one's main interest is RNA-seq, R will probably be more…
Comment: Which language use as a beginner in Bioinformatics and Computational genomics by Brian Bushnell 19k
It depends on specifically what you will be doing. But IMO the order of importance is Bash > Python > R.
Comment: Bam files generated with STAR cause a segmentation fault core dump error when us by bkffadia • 0
![Galaxy Command Line][1] [1]: /media/images/8c45586a-e3e3-46dd-b06b-a9788a6e
Comment: RNA seq by Istvan Albert 99k
there is no need to "average" anything, the point of replicates and RNA-Seq in general, is to measure the same thing several times and use …
Answer: Which language use as a beginner in Bioinformatics and Computational genomics by Istvan Albert 99k
I would say every scientist needs to know R - so if you don't know R it would serve you well to learn it. In my opinion Python is not we…
Answer: using RMA normalized microarray in Limma by ATpoint 78k
Arrays do not have counts. RMA-proceased data are fine. See limma user guide.
Comment: RNA seq by ATpoint 78k
What is the question? I assume you googled 'differential RNA-seq' and tried the obvious tools such as DESeq2 and limma?
Answer: Can't install hisat2 with miniconda by Istvan Albert 99k
You have installed the wrong version of conda. Even on M1 (arm64 CPU) you need to be using the Intel-based (x64 CPU) conda installer. So …
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