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383 results • Page 1 of 8
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238
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176
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90k
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73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 6 months ago by 41k • written 8.3 years ago by ★ 4.7k
132
votes
123
replies
34k
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 8 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 8 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 6.0 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 8 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 9 months ago by 41k • written 6.2 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 8 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 28 days ago by 41k • written 10.1 years ago by ★ 7.8k
196
votes
44
replies
70k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 10 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 8 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 7.4 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
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 5.4 years ago by ★ 1.3k
146
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 10.6 years ago by 6.0k
288
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
9.9k
views
10 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 5 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 8 months ago by 41k • written 4.3 years ago by 8.4k
48
votes
30
replies
9.3k
views
11 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 4 weeks ago by 78k • written 7.7 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 7.7 years ago by 20k
64
votes
26
replies
13k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 8 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 8 months ago by 41k • written 4.7 years ago by 16k
72
votes
26
replies
27k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 9 months ago by 41k • written 9.8 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 7.3 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
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
88
votes
22
replies
83k
views
14 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 4 months ago by • 0 • written 5.4 years ago by ▴ 580
18
votes
22
replies
8.4k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 9 weeks ago by ▴ 20 • written 4.0 years ago by 8.4k
84
votes
21
replies
20k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 8 months ago by 41k • written 3.1 years ago by 3.1k
142
votes
21
replies
29k
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
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 8 months ago by 41k • written 4.5 years ago by ★ 16k
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
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 11.6 years ago by 11k
47
votes
19
replies
13k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control fastqc
updated 10 months ago by 41k • written 10.8 years ago by 99k
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
23
votes
19
replies
6.4k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
fastq mutation cancer target
updated 7 months ago by 41k • written 7.2 years ago by ★ 2.5k
8
votes
19
replies
13k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
mysql orthomcl
updated 8 months ago by 41k • written 9.0 years ago by ▴ 600
26
votes
17
replies
7.3k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv
updated 14 months ago by 41k • written 9.3 years ago by 6.0k
12
votes
17
replies
2.6k
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 10.0 years ago by 20k
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 8.1 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 15 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 8 months ago by 41k • written 7.3 years ago by 26k
34
votes
15
replies
6.0k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 8 months ago by 41k • written 4.5 years ago by ★ 9.3k
34
votes
15
replies
19k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 8 months ago by 41k • written 7.2 years ago by ▴ 310
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
63
votes
15
replies
13k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 6 months ago by 41k • written 5.1 years ago by 16k
7
votes
14
replies
3.2k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 13 months ago by • 0 • written 21 months ago by ▴ 30
383 results • Page 1 of 8
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Recent Replies
Comment: Annotate Unplaced Scaffold with Chromosome Information by cmdcolin ★ 3.4k
I think there are tools like ragtag https://github.com/malonge/RagTag that could help. you can also align your reads back to your new assem…
Comment: Error with .vcf files when using Truvari by Pierre Lindenbaum 158k
> Despite attempts using awk and sed to add 'chr' to the truth file, none have been successful. 1) we cannot see the code you used 2) use…
Comment: An incomprehensible error with R package gggenes by ATpoint 78k
It's not stupid, just a bit lazy ;-)
Comment: Adding functional annotation and meta-data of MAKER/BRAKER GFF by ben@f • 0
Hi, did you find an effective solution for this problem? beside Agat and
Comment: An incomprehensible error with R package gggenes by alice005201314 • 0
Thank you. I asked a stupid question.
Answer: An incomprehensible error with R package gggenes by ATpoint 78k
First hit on google: https://stackoverflow.com/questions/73935357/error-in-grid-callc-convert-x-as-integerwhatfrom-as-integerwhatto-vie
Answer: Should I scale all genes in single cell Seurat? by antonioggsousa 3.0k
Hi, Scaling all features might be useful to plot genes that are not among the 2k HVG in a heatmap. Otherwise than that, I never encounter…
Comment: How to filter .fasta file based on conditional statement by rob_DNA ▴ 20
Oh wow that was a bit stupid.. I downloaded 39.06 but I accidentally used 39.01... anyway, thank you very much for your help!! I now used t…
Comment: How can I map coordinates between two strains of yeast? by Jimmy ▴ 10
Yes (S. cerevisiae)
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by GenoMax 136k
> less than 100 for some samples Hmm. That is surprising but then in light of that fact ~20% recovery of cells does not sound bad.
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by newbee ▴ 40
Thanks for raising these valid points. I do not have the answer right now. Lately, I heard from the PI that they started with a small numbe…
Comment: How to get multiple protein domain database domain name from id's by GenoMax 136k
A list of InterPro domains is available: https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/entry.list
Answer: DIAMOND tutorial by GenoMax 136k
`DIAMOND` has a wiki page: https://github.com/bbuchfink/diamond/wiki Links for DIAMOND papers are here: https://github.com/bbuchfink/diamo…
Comment: How to do simple pathway analysis? by AK ★ 2.2k
Hi [he1k](https://www.biostars.org/u/139817/), Please use the following script which downloads and parses the keg data on the fly: [keg_hi…
Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison by CTLong ▴ 20
That's what I would assume, because we are not taking into account cross sample differences here. Thanks
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