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319 results • Page 1 of 7
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238
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176
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91k
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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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 10.9 years ago by 6.0k
51
votes
14
replies
80k
views
10 follow
Tutorial: Using R in Conda
R
updated 9 months ago by 41k • written 3.4 years ago by ▴ 780
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
36
votes
14
replies
32k
views
14 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 4 weeks ago by ▴ 50 • written 3.3 years ago by ▴ 160
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
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
8.1k
views
10 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 5 weeks ago by • 0 • written 17 months ago by 78k
319 results • Page 1 of 7
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Answer: Autocompleting paths within scripts
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Recent Replies
Comment: How should I run ssgsea analysis ? by Ram 41k
Just add a statement to your comments stating that the text was generated using ChatGPT - it is a good tool but it's not aware of its own s…
Comment: Autocompleting paths within scripts by DanielEB_fisk ▴ 20
Yep, sorry, you are right it is not a bioinformatics question. I asked here because it relates with the work we do anyway.
Comment: autodock vina on mac by Ram 41k
That section is for after you have virtualbox set up. You may have to run a really old version of macOS within the virtualbox, so be prepar…
Comment: ChatGPT optimized for bioinformatics questions by Ram 41k
I understand. The purpose of my comment is to serve as feedback.
Comment: How can I obtain the DNA sequences of each CDS for several genbank files? by Ram 41k
Look into passing command line parameters to a python script. You can pass the input file name as a parameter to the script and execute the…
Answer: Autocompleting paths within scripts by Michael 53k
Not really a Bioinformatics question but generally very useful: [vim can do that][1] [type some prefix of path]<Ctrl-x><Ctrl-f> This…
Comment: How can I obtain the DNA sequences of each CDS for several genbank files? by Raphaëlle • 0
Hello, Thank you very much for your quick reply. That was indeed the issue! Another question: is there a simple way of automating this …
Answer: Cluster sub-set analysis using Seurat by j.gleixner ▴ 10
There now is also `Seurat::FindSubCluster`
Comment: How can i control the cluster number in scRNASeq clustering by Seurat package by j.gleixner ▴ 10
There is now also Seurat::BuildClusterTree that makes this easier.
Answer: How can i control the cluster number in scRNASeq clustering by Seurat package by j.gleixner ▴ 10
If you want to get a certain number of clusters without resorting to trying different settings for the resolution parameter, you can firs…
Answer: How to speed-up to contruct phylogenetic tree by Nelo ▴ 20
I will also try this `fasttree`
Comment: i ues schicexplorer's hicbuildmatrix code complains that two sam files do not ha by 1125195245 • 0
I tried using bowtie2's --reorder command to output a sam file for each of the two files, and then used both sam files to build the matrix,…
Comment: How to speed-up to contruct phylogenetic tree by Nelo ▴ 20
I used MEGA CC (comand line option) but there is no option to specify threads in its `--help` manual . And default thread is 4
Comment: How to speed-up to contruct phylogenetic tree by Nelo ▴ 20
The average length of fasta sequences is ~300aa length. I can't exclude any sequences as I have to provide them nomenclature aslo on the ba…
Comment: How to speed-up to contruct phylogenetic tree by Nelo ▴ 20
I used Raxml for a trial fasta file of about only 33 sequences as: `raxmlHPC-PTHREADS-AVX -f a -T 80 -m PROTGAMMAWAG -n test1 -s bittergou…
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