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90k
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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 8.4 years ago by ★ 4.7k
132
votes
123
replies
35k
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 9 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 9 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 6.1 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 9 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 10 months ago by 41k • written 6.3 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 9 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 5 weeks ago by 41k • written 10.2 years ago by ★ 7.8k
196
votes
44
replies
70k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 11 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 9 months ago by 41k • written 6.2 years ago by ★ 1.4k
18
votes
40
replies
17k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 3.4 years ago by • 0 • written 7.5 years ago by ▴ 170
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
147
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 10.7 years ago by 6.0k
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
290
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 9 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 6 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 5 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 7.8 years ago by 20k
72
votes
27
replies
27k
views
16 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 7 days ago by • 0 • 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 9 months ago by 41k • written 6.2 years ago by 86k
65
votes
26
replies
13k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 9 months ago by 41k • written 4.8 years ago by 16k
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
137
votes
25
replies
81k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 20 months ago by 41k • written 11.6 years ago by ★ 4.2k
88
votes
22
replies
84k
views
14 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 5 months ago by • 0 • written 5.4 years ago by ▴ 580
18
votes
22
replies
8.5k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 11 weeks ago by ▴ 20 • written 4.0 years ago by 8.4k
142
votes
21
replies
30k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 19 months ago by 41k • written 9.0 years ago by ★ 1.6k
84
votes
21
replies
20k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 9 months ago by 41k • written 3.2 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 9 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 8 months ago by 41k • written 7.2 years ago by ★ 2.5k
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 11 months ago by 41k • written 10.8 years ago by 99k
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 9 months ago by 41k • written 9.1 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 11.7 years ago by 11k
26
votes
17
replies
7.4k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv
updated 15 months ago by 41k • written 9.3 years ago by 6.0k
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 10.1 years ago by 20k
12
votes
17
replies
2.7k
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
8
votes
17
replies
2.9k
views
Tutorial: Simple approach to RNA-seq (T-Bioinfo platform)
alignment next-gen-sequencing RNA-seq
updated 15 months ago by 41k • written 8.2 years ago by ▴ 340
42
votes
16
replies
23k
views
15 follow
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC varscan2 CNV copy-number
updated 16 months ago by 41k • written 8.2 years ago by ★ 2.4k
99
votes
16
replies
32k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 9 months ago by 41k • written 7.4 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
6.0k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 9 months ago by 41k • written 4.5 years ago by ★ 9.3k
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 9 months ago by 41k • written 7.2 years ago by ▴ 310
75
votes
14
replies
15k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 10 months ago by 41k • written 10.6 years ago by 9.7k
385 results • Page 1 of 8
Recent Votes
Answer: How to speed-up to contruct phylogenetic tree
Comment: How to speed-up to contruct phylogenetic tree
Answer: Renaming fasta files with their headers
Comment: What apps can read large FASTQ files on Windows?
Answer: Renaming fasta files with their headers
Answer: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 202
Answer: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 202
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Recent Replies
Comment: Renaming fasta files with their headers by sebabiokr ▴ 10
Yes, Its perfectly working.. It will be useful if you share concat command too if there are same genes in the fasta file Thank you
Answer: Renaming fasta files with their headers by shenwei356 8.3k
I've got a general method, but you need to have some basic knowledge of regular expressions. If not, please learn them for 30 minutes: -…
Comment: Renaming fasta files with their headers by liorglic ★ 1.3k
It's hard to understand what your input and desired output look like. Please edit your original question so it includes a clear explanation…
Comment: SRA toolkit (NCBI) - sra to fasta by ATpoint 78k
Can be 23 or 109, it does not matter.
Comment: Renaming fasta files with their headers by sebabiokr ▴ 10
Thank you for your code, but i have a fasta file which contains [gene=rps12] ids, so i want to rename the header with gene id alone like >r…
Answer: How to speed-up to contruct phylogenetic tree by Mensur Dlakic ★ 25k
It depends on how long your protein is. Generally speaking, it shouldn't take weeks or months. Trees with more than ~100 branches are very …
Comment: How to speed-up to contruct phylogenetic tree by liorglic ★ 1.3k
Is there a specific reason you need to use MEGA? Maybe try another software which might be faster (e.g. PhyML, RaxML, IQ-TREE). Also, do yo…
Answer: Renaming fasta files with their headers by liorglic ★ 1.3k
Assuming that you have a directory containing multiple files with `.fasta` extension, each containing one record, you can do something like…
Comment: What are the methods to correlate/study metabolomics data to proteomics data? by LauferVA 3.8k
thank you, @wuschel, for the comprehensive reply.
Comment: Renaming fasta files with their headers by sebabiokr ▴ 10
i tried this command awk -F 'gene=|]|[.]{1}' '/^>/ {print $2}' 7seqNC_018552.1cds.fasta > 7NC_018552.fasta got only gene name alone wit…
Answer: Converting a .frq file to a data frame? by zau saa ▴ 70
simply add a word to line 1 as the name of column 6
Comment: SRA toolkit (NCBI) - sra to fasta by Sanjukta • 0
Hi there, will it be an issue if we do not mention 60?
Comment: Renaming fasta files with their headers by sebabiokr ▴ 10
Yes there are many answer in this forum but they are specific to header line. it doesnot work with my header line and its difficult for me …
Answer: What are the methods to correlate/study metabolomics data to proteomics data? by WUSCHEL ▴ 740
There are various methods to correlate and study metabolomics data to proteomics data. These methods can be broadly categorized into: 1. C…
Comment: Renaming fasta files with their headers by Mensur Dlakic ★ 25k
This type of question is among the most frequently asked on this forum. Searching through previous posts should give you several different …
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