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234
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82k
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73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 7 weeks ago by 37k • written 7.4 years ago by ★ 4.6k
128
votes
122
replies
26k
views
23 follow
Tutorial: Survival analysis with gene expression
survival analysis cox geo gene expression Tutorial
updated 3 months ago by • 0 • written 4.1 years ago by 84k
89
votes
104
replies
31k
views
24 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Tutorial 1000 genomes PCA PLINK
updated 8 weeks ago by ▴ 160 • written 4.3 years ago by 84k
75
votes
70
replies
15k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment Tutorial david
updated 10 months ago by • 0 • written 4.8 years ago by 84k
141
votes
68
replies
41k
views
18 follow
Tutorial: Network plot from expression data in R using igraph
R Tutorial microarray RNA-Seq network
updated 5 months ago by • 0 • written 5.0 years ago by 84k
115
votes
66
replies
38k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera ENA fastq-dump Tutorial Fastq
5 months ago by ATpoint 66k
72
votes
60
replies
22k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000 genomes PCA VCF PLINK Tutorial
updated 6 days ago by • 0 • written 5.2 years ago by 84k
60
votes
49
replies
38k
views
22 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
R plotly volcano plot Tutorial
updated 19 months ago by 37k • written 6.2 years ago by ★ 3.3k
72
votes
48
replies
15k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
bwa alignment ngs tutorial Tutorial
updated 8 months ago by 37k • written 9.8 years ago by 33k
194
votes
44
replies
67k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
tutorial bioconductor microarray analysis tutorial Tutorial
updated 8 weeks ago by 37k • written 10.2 years ago by 20k
78
votes
41
replies
27k
views
24 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 14 days ago by • 0 • written 9.1 years ago by ★ 7.6k
59
votes
41
replies
17k
views
16 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
arrow pbalign pacbio polishing smrt limk Tutorial
updated 2.6 years ago by • 0 • written 5.2 years ago by ★ 1.4k
17
votes
40
replies
15k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
run easy orthomcl all-v-all mcl Tutorial
updated 2.1 years ago by ★ 2.0k • written 6.4 years ago by ▴ 160
273
votes
39
replies
159k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA download GEO bam
updated 7 months ago by 37k • written 8.3 years ago by 20k
146
votes
35
replies
57k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics Tutorial next-gen
updated 7 months ago by • 0 • written 10.0 years ago by ★ 1.6k
83
votes
34
replies
14k
views
21 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
R pathway enrichment active subnetwork Tutorial
updated 4 months ago by 37k • written 4.5 years ago by ★ 1.3k
143
votes
34
replies
50k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
mutation maf tcga cancer music Tutorial
updated 7 months ago by 37k • written 9.6 years ago by 5.8k
273
votes
33
replies
88k
views
24 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates tutorial Tutorial
updated 10 months ago by ▴ 100 • written 9.1 years ago by 20k
42
votes
33
replies
6.4k
views
8 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
meta how-to documentation Tutorial
2.0 years ago by Ram 37k
11
votes
31
replies
4.3k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
gene geneset abinitio Tutorial genome
6 weeks ago by Juke34 7.4k
82
votes
28
replies
27k
views
19 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
GenVisR BioConductor R Graphics Tutorial
updated 4 weeks ago by 123k • written 6.7 years ago by 20k
62
votes
26
replies
9.8k
views
11 follow
Tutorial: Generating consensus sequence from bam file
bam consensus fasta Tutorial
updated 18 months ago by ▴ 180 • written 3.8 years ago by 15k
63
votes
26
replies
11k
views
7 follow
Tutorial: Parallel processing in R
R Tutorial biocparallel mclapply foreach
3.1 years ago by Kevin Blighe 84k
68
votes
26
replies
23k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
rna-seq tutorial Tutorial
updated 3 months ago by • 0 • written 8.8 years ago by 96k
58
votes
25
replies
35k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC TCGA Download methylation Tutorial
updated 4.1 years ago by 66k • written 6.4 years ago by ★ 9.2k
132
votes
25
replies
72k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 8 months ago by 37k • written 10.6 years ago by ★ 4.2k
94
votes
25
replies
31k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality fastq trimming qc tutorial Tutorial
updated 9 months ago by 37k • written 10.2 years ago by 96k
9
votes
23
replies
8.0k
views
7 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
orthomcl ubuntu linux mysql Tutorial
4.5 years ago by vimalkvn ▴ 310
142
votes
21
replies
28k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 7 months ago by 37k • written 8.0 years ago by ★ 1.6k
79
votes
21
replies
12k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
enrichment microarray Tutorial GSEA RNA-Seq
updated 3 months ago by • 0 • written 2.1 years ago by 2.8k
12
votes
20
replies
11k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
seurat single cell RNA-Seq TCR Tutorial
18 months ago by jared.andrews07 ★ 14k
17
votes
19
replies
6.2k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat Tutorial annotation
13 hours ago by Juke34 7.4k
8
votes
19
replies
12k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
orthomcl mysql no root local Tutorial
updated 9 months ago by 37k • written 8.0 years ago by ▴ 580
89
votes
19
replies
30k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
classification microarray expression bioconductor Tutorial
updated 10 weeks ago by 37k • written 9.1 years ago by 20k
51
votes
19
replies
41k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
chip-seq rna-seq bigwig visualization ucsc tutorial Tutorial
updated 4 months ago by 37k • written 10.6 years ago by 11k
47
votes
19
replies
12k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
fastqc qualitycontrol tutorial Tutorial
updated 9.8 years ago by ▴ 140 • written 9.8 years ago by 96k
42
votes
19
replies
7.0k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software tutorial Tutorial
9.8 years ago by Daniel Standage 4.1k
23
votes
19
replies
5.4k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
mutation fastq cancer target Tutorial
updated 4.9 years ago by • 0 • written 6.2 years ago by ★ 2.4k
73
votes
18
replies
65k
views
12 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
samtools bcftools htslib Tutorial
updated 2 days ago by 37k • written 4.4 years ago by ▴ 500
8
votes
17
replies
2.2k
views
Tutorial: Simple approach to RNA-seq (T-Bioinfo platform)
alignment next-gen-sequencing RNA-seq
updated 3 months ago by 37k • written 7.2 years ago by ▴ 340
12
votes
17
replies
2.1k
views
Tutorial: How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola bwa Tutorial
7.5 years ago by Istvan Albert 96k
26
votes
17
replies
6.5k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv
updated 12 weeks ago by 37k • written 8.3 years ago by 5.9k
98
votes
16
replies
29k
views
18 follow
Tutorial: Heatmaps in R
Tutorial R heatmap
7 months ago by Jean-Karim Heriche 26k
42
votes
16
replies
20k
views
15 follow
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC varscan2 CNV copy-number
updated 4 months ago by 37k • written 7.2 years ago by ★ 2.3k
33
votes
16
replies
14k
views
10 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
classification tutorial Tutorial
5.6 years ago by Obi Griffith 20k
34
votes
15
replies
4.5k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf Tutorial
updated 9 months ago by 37k • written 3.5 years ago by ★ 9.2k
24
votes
15
replies
7.7k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
bioinformatics training tutorial Tutorial
8 months ago by Medhat 9.4k
34
votes
15
replies
17k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
R TCGA GDC next-gen Tutorial
updated 3.8 years ago by ▴ 30 • written 6.2 years ago by ▴ 310
57
votes
15
replies
11k
views
Tutorial: Which human reference genome should I use?
genome alignment assembly Tutorial
4.1 years ago by finswimmer 15k
7
votes
14
replies
1.6k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 5 weeks ago by • 0 • written 9 months ago by ▴ 30
346 results • Page 1 of 7
Recent Votes
A: Extract base information from aligned reads in a sam file
A: Extract base information from aligned reads in a sam file
A: Combine paired-end fastq files
A: Why do the number of domains in these two orthologs differ? Why is hmmscan annot
SNPsift
C: How to sort a FASTA file and (its) BAM file in the same order?
A: What proportion of the (coding) genome is actually expressed at any given time?
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Recent Replies
Comment: Transform Data into DNA picture by anasjamshed1994 ▴ 120
what does genotype mean in rsid? What does it indicate?![rsid][1] [1]: /media/images/7638ed2f-7ed2-4cc0-8ce4-58ab0226
Comment: Any good tools for biological annotation of ChIP-seq broadpeak (H3K9me3, H3K27me by hiroyuki.kato.911 • 0
Thanks! I got it!
Answer: Inquiry related to processing multiple db file simulataneously by Pierre Lindenbaum 151k
how about calling `dbDisconnect` after `dbGetQuery` ?
Answer: Automated way to pull representative/RefSeq genome using full species name? by MirianT_NCBI ▴ 340
Hi Alex, You can use [NCBI Datasets][1]. `datasets` allows users to download genome and associated annotation files as a data package. I…
Comment: bedtools getfasta error: Error: malformed GFF entry at line 15. Coordinate detec by Pierre Lindenbaum 151k
but it's decoded AS a GFF/GTF file because bedtools can see columns 4 and 5 are integers. move columns 4 and 5 to columns 2 and 3 to create…
Comment: BioMart dropping and duplicating Ensembl IDs while retrieving corresponding gene by Matthias Zepper 2.4k
I already linked the MANE website above. Navigate to *Accessing MANE data* and download [this file][1]. It is an equivalence table and cont…
Comment: bedtools getfasta error: Error: malformed GFF entry at line 15. Coordinate detec by Simone • 0
It's not a GFF file, it's a TSV annotation file, output from BUSCO. The annotations are coordinates for BUSCO genes. I've tried using BEDOP…
Comment: What are Supplementary Reads? by cmdcolin ★ 2.5k
Large insertions or deletions can cause supplementary alignments to be created, even though it is still linear. But, minimap2 will try to a…
Comment: How to find rna strand direction before alignment? by swbarnes2 12k
OP said he didn't want to align. That script takes a bad and a bam as input.
Comment: GO enrichment analysis graphs after goseq: any easy solutions? by afsanarupa1 • 0
Please can you tell me details step by step how can these types of graphs be generated using output files from goseq as stated in trinity p…
Comment: What's Supplementary Reads? by Istvan Albert 96k
one concept the "linearity" of the alignment is important. A chimeric alignment is found to be "chimeric" if the entire read is represented…
Answer: How to find rna strand direction before alignment? by KoppesEA ▴ 80
[https://rseqc.sourceforge.net/][1] infer_experiment.py [1]: https://rseqc.sourceforge.net/ "RSEQC"
Answer: What's Supplementary Reads? by cmdcolin ★ 2.5k
I wrote a blogpost discussing some topics related to supplementary reads. Especially with long reads, supplementary reads are often "split …
Comment: For loop for aligning multiple paired end fastq files by Ram 37k
What did you have to do to get it working?
Comment: For loop for aligning multiple paired end fastq files by kcarery • 0
Thank you for your support, it is finally working
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