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Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 5 months ago by 38k • written 7.7 years ago by ★ 4.6k
130
votes
123
replies
29k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 7 days ago by ★ 1.1k • written 4.4 years ago by 84k
92
votes
105
replies
34k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 16 days ago by 38k • written 4.6 years ago by 84k
75
votes
70
replies
16k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 15 days ago by 38k • written 5.1 years ago by 84k
144
votes
68
replies
43k
views
18 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 16 days ago by 38k • written 5.4 years ago by 84k
116
votes
66
replies
40k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 16 days ago by 38k • written 4.7 years ago by 70k
72
votes
60
replies
23k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 6 weeks ago by 38k • written 5.6 years ago by 84k
60
votes
52
replies
39k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 15 days ago by 38k • written 6.5 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?
ngs alignment bwa
updated 4 weeks ago by 38k • written 10.1 years ago by 33k
194
votes
44
replies
68k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 11 weeks ago by 38k • written 10.5 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 15 days ago by 38k • written 5.5 years ago by ★ 1.4k
78
votes
41
replies
28k
views
24 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 4 months ago by • 0 • written 9.4 years ago by ★ 7.7k
17
votes
40
replies
16k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 15 days ago by 38k • written 6.8 years ago by ▴ 160
276
votes
39
replies
164k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 5 days ago by 38k • written 8.6 years ago by 20k
146
votes
35
replies
58k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 4 weeks ago by 38k • written 10.3 years ago by ★ 1.6k
83
votes
34
replies
15k
views
21 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
active-subnetwork enrichment pathway R
updated 20 days ago by 38k • written 4.8 years ago by ★ 1.3k
145
votes
34
replies
51k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 4 weeks ago by 38k • written 10.0 years ago by 5.9k
275
votes
33
replies
92k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 29 days ago by 38k • written 9.4 years ago by 20k
42
votes
33
replies
6.8k
views
8 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
meta how-to documentation
15 days ago by Ram 38k
12
votes
31
replies
4.7k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 20 days ago by 38k • written 3.6 years ago by 7.8k
82
votes
28
replies
28k
views
19 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 6 weeks ago by 38k • written 7.1 years ago by 20k
68
votes
26
replies
24k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 27 days ago by 38k • written 9.1 years ago by 97k
64
votes
26
replies
11k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 15 days ago by 38k • written 5.5 years ago by 84k
64
votes
26
replies
11k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 16 days ago by 38k • written 4.1 years ago by 16k
136
votes
25
replies
75k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 11 months ago by 38k • written 10.9 years ago by ★ 4.2k
94
votes
25
replies
31k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 5 weeks ago by 38k • written 10.5 years ago by 97k
58
votes
25
replies
36k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 12 days ago by 38k • written 6.7 years ago by ★ 9.3k
9
votes
23
replies
8.3k
views
7 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
orthomcl ubuntu linux mysql Tutorial
4.8 years ago by vimalkvn ▴ 310
18
votes
22
replies
7.1k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 15 days ago by 38k • written 3.3 years ago by 7.8k
142
votes
21
replies
29k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 10 months ago by 38k • written 8.3 years ago by ★ 1.6k
82
votes
21
replies
15k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 20 days ago by 38k • written 2.5 years ago by 2.9k
82
votes
21
replies
71k
views
13 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 5 weeks ago by ★ 2.9k • written 4.7 years ago by ▴ 540
12
votes
20
replies
11k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 15 days ago by 38k • written 3.8 years ago by ★ 14k
51
votes
19
replies
41k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization bigwig chip-seq rna-seq
updated 5 weeks ago by 38k • written 11.0 years ago by 11k
23
votes
19
replies
5.7k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
mutation fastq cancer target Tutorial
updated 5.2 years ago by • 0 • written 6.5 years ago by ★ 2.4k
89
votes
19
replies
30k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray bioconductor expression classification
updated 28 days ago by 38k • written 9.4 years ago by 20k
42
votes
19
replies
7.1k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 4 weeks ago by 38k • written 10.1 years ago by 4.1k
8
votes
19
replies
12k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
mysql orthomcl
updated 20 days ago by 38k • written 8.4 years ago by ▴ 580
47
votes
19
replies
12k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control fastqc
updated 11 weeks ago by 38k • written 10.1 years ago by 97k
8
votes
17
replies
2.3k
views
Tutorial: Simple approach to RNA-seq (T-Bioinfo platform)
alignment next-gen-sequencing RNA-seq
updated 7 months ago by 38k • written 7.5 years ago by ▴ 340
26
votes
17
replies
6.7k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv
updated 6 months ago by 38k • written 8.6 years ago by 5.9k
12
votes
17
replies
2.2k
views
Tutorial: How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola bwa
updated 3 months ago by 38k • written 7.8 years ago by 97k
99
votes
16
replies
30k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 15 days ago by 38k • written 6.6 years ago by 26k
33
votes
16
replies
15k
views
10 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 28 days ago by 38k • written 9.4 years ago by 20k
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 7 months ago by 38k • written 7.5 years ago by ★ 2.3k
24
votes
15
replies
7.9k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
course training mooc
updated 4 weeks ago by 38k • written 10.2 years ago by 9.5k
34
votes
15
replies
5.0k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 15 days ago by 38k • written 3.8 years ago by ★ 9.3k
59
votes
15
replies
11k
views
Tutorial: Which human reference genome should I use?
genome alignment assembly Tutorial
4.4 years ago by finswimmer 16k
34
votes
15
replies
18k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 14 days ago by 38k • written 6.5 years ago by ▴ 310
30
votes
14
replies
15k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 4 weeks ago by 38k • written 10.2 years ago by 5.9k
353 results • Page 1 of 8
Recent Votes
Answer: How can I use bcftools mpileup or an alternative to find ALL variants without an
Answer: What is the NCBI's definition of an "atypical genome"?
Comment: GO enrichment analysis
Comment: GO enrichment analysis
Answer: What is the NCBI's definition of an "atypical genome"?
A: Why is RNA-Seq or cDNA used to detect gene fusions instead of gDNA?
Answer: Somatic truth set
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Recent Awards • All
Popular Question to Bogdan ★ 1.3k
Popular Question to pavelasquezv ▴ 50
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Recent Replies
Answer: Align miRNA library (small RNA-seq) without trimming by Ming Tommy Tang ★ 2.9k
bowtie 1 is good for short read < 50bp, how long is your read? bowtie2 is better for reads > 50 bp
Comment: Differences in RNAseq Variant Calling and Allele Specific Expression by afei • 0
Hi! I'm also confused by this. And the site (https://gatkforums.broadinstitute.org/gatk/categories/gatk-support-forum) is closed. Have you …
Comment: Variant caller reports a homozygous variant genotype, but more reads are associa by rebeliscu ▴ 50
Indeed, I thought the quality might be a factor. Still, given the information, it seems odd to me that that call was made. Thanks for you…
Answer: How can I use bcftools mpileup or an alternative to find ALL variants without an by cfos4698 ▴ 730
To generate a VCF file one would normally pipe the input of an `mpileup` command into an actual `call` command. For example: ``` bcftools …
Answer: PTM-aware protein folding / docking by Mensur Dlakic ★ 23k
Your assumption is correct - AlphaFold pTM has nothing to do with post-translational modifications. See [**here**][1]. Not to discourage…
Answer: Admixture cv error by Declan • 0
I had this issue today and was able to resolve it by changing the random seed Admixture uses by adding `-s time` (which sets the random see…
Answer: Total No of Genes of GENCODE Release 43 by ahmad • 0
The following is the correct code gtf_43<-rtracklayer::import('gencode.v43.primary_assembly.annotation.gtf') dtgtf_43<-data.frame(gtf_4…
Comment: Total No of Genes of GENCODE Release 43 by ahmad • 0
Hello, thanks for replying, by mistake I paste the wrong code. the following is the corrected gtf_43<-rtracklayer::import('gencode.v43…
Comment: Kallisto bustools for scRNA-seq by dsull ★ 4.0k
I have no idea what that is besides a bunch of jumbled sequences. You'll need look up the structure of the reads / library from wherever yo…
Comment: Aberrant splicing in bulk RNAseq by dsull ★ 4.0k
First thing: kallisto cannot interface with UMI-tools (kallisto doesn't use read headers and therefore you're stuck with "the kallisto way"…
Comment: Using Copy Number Alterations detected in other studies for the same tumor cell by lethalfang ▴ 90
There is some somatic SV study on these HCC1395: https://doi.org/10.1186/s13059-022-02816-6. There is also a CNA preprint from years ago b…
Comment: Somatic truth set by lethalfang ▴ 90
Just in case things are hard to find, for the WGS/WES, these are the data (what the file names mean: https://sites.google.com/view/seqc2/ho…
Comment: How to get subset of a Seurat object based on metadata? by jv ★ 1.0k
Hmm, not sure why `subset` doesn't match to '0:CD8 T cell' but maybe it's the ":"? An alternative option is the following: ``` idx <- whi…
Comment: GO enrichment analysis by Jeremy ▴ 780
g:Profiler has an Arabidopsis option: [g:Profiler][1] [1]: https://biit.cs.ut.ee/gprofiler/gost
Answer: Any tips in landing a bioinformatic job? by Carambakaracho ★ 3.2k
The first job is a nightmare and you will need some luck. I understand you're looking for an industry offering. Unfortunately I've worked o…
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