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Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 11 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 9 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 28 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 9 days ago by • 0 • written 5.0 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
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
18 days ago by Ram 39k
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
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
136
votes
25
replies
77k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 14 months ago by 39k • written 11.1 years ago by ★ 4.2k
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 6.9 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 17 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
142
votes
21
replies
29k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 13 months ago by 39k • written 8.5 years ago by ★ 1.6k
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
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
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
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
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
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
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
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 4 weeks ago by 129k • written 9.5 years ago by 20k
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
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 10 months ago by 39k • written 7.7 years ago by ★ 2.3k
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
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
59
votes
15
replies
12k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 11 days ago by 39k • written 4.7 years ago by 16k
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
30
votes
14
replies
15k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 3 months ago by 39k • written 10.3 years ago by 5.9k
357 results • Page 1 of 8
Recent Votes
Answer: Perl script running slow with big files
C: Bedtools problem : It looks as though you have less than 3 columns at line: 1.
A: Forward And Reverse Strand Conventions
Comment: hisat2 Error 137
Comment: NCBI API, Perl
Comment: Is hg38 on the multiz 30-way alignment inaccurate?
Answer: Is it possible to add a dendrogram as a top annotation using ComplexHeatmap ?
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Recent Replies
Comment: Is hg38 on the multiz 30-way alignment inaccurate? by Maximilian Haeussler ★ 1.5k
Can you provide an example? Which MAF file are you referring to, on the UCSC and Ensembl side. I can imagine a dozen different things that …
Comment: Trying to edit VCF file by Pierre Lindenbaum 154k
are they present in Fall22C.txt ?
Comment: Trying to edit VCF file by peavy • 0
Y Z and AA ideally wont be there or come up in the vcf file if I removed them proper so I'm wondering what the issue is in the initial code.
Comment: Trying to edit VCF file by Pierre Lindenbaum 154k
> I noticed that there was still columns for what I removed from the file. so, what should we see in your image ??
Comment: Trying to edit VCF file by peavy • 0
![The last 3 columns are what I thhought I deleted ][1] [1]: /media/images/709ceea6-da38-47e3-b4ab-13727837
Comment: NCBI API, Perl by GenoMax 129k
Using EntrezDirect: $ esearch -db nuccore -query LOC105370256 | efetch -format acc | grep -v NC | xargs -n 1 sh -c 'efetch -db nuccore…
Comment: calculate p value and associated z score for snp-gene pair by LChart 2.6k
I think researchers would agree that FDR > 0.05 is not significant, though some would argue FDR between 0.05 and 0.1 is OK for an initial f…
Comment: Trying to edit VCF file by Pierre Lindenbaum 154k
> When I opened the vcf in excel I noticed that there was still columns for what I removed from the file. please, explain, show the data.…
Comment: hisat2 Error 137 by Forough ▴ 10
Thank you very much for sending the like. I will try it.
Comment: Which method is the best for using in "dba.count" in Diffbind R package by Jo • 0
Thank you for all the helpful advice and explanations. Can you further explain this part: > "The default normalization factors (based sol…
Comment: VEP tab/vcf - Different output by Ram 39k
I don't think so, no. EnsEMBL seems to have come up with a verbose explanation for why they don't want to put in the effort.
Comment: VEP tab/vcf - Different output by Jeremy Leipzig 21k
is there any way to report the VCF-style ref and alt in the VEP tabular output?
Comment: Is hg38 on the multiz 30-way alignment inaccurate? by Daniel ▴ 30
Thank you! If I understand correctly, it's possible that the coordinates/sequences may not be the same anymore, because the maf files use t…
Comment: NCBI API, Perl by alessandro.alma00 • 0
Sorry i didn't want to be rude.. Thank you for helping me, im sorry but its the first time I use API tbh... i will like to retrieve the seq…
Comment: How to perform statistical analysis of label free experiment using results from by Ram 39k
Do not add answers unless you're actually answering the question. Use `Add Comment` instead. I've moved your post this time, be careful in …
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