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323 results • Page 1 of 7
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Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 4 months ago by 40k • written 8.2 years ago by ★ 4.7k
132
votes
123
replies
33k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 6 months ago by ★ 1.1k • written 5.0 years ago by 86k
93
votes
105
replies
39k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 6 months ago by 40k • written 5.1 years ago by 86k
76
votes
70
replies
17k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 6 months ago by 40k • written 5.6 years ago by 86k
146
votes
70
replies
46k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 4 weeks ago by ▴ 260 • written 5.9 years ago by 86k
116
votes
66
replies
43k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 6 months ago by 40k • written 5.2 years ago by 77k
73
votes
60
replies
25k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 7 months ago by 40k • written 6.1 years ago by 86k
60
votes
52
replies
41k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 6 months ago by 40k • written 7.0 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 7 months ago by 40k • written 10.6 years ago by 33k
84
votes
47
replies
30k
views
28 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 3 days ago by 40k • written 10.0 years ago by ★ 7.7k
196
votes
44
replies
70k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 8 months ago by 40k • written 11.0 years ago by 20k
59
votes
43
replies
19k
views
18 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign pacbio arrow smrt-limk
updated 6 months ago by 40k • written 6.0 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 6 months ago by 40k • written 7.3 years ago by ▴ 170
282
votes
39
replies
174k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 6 months ago by 40k • written 9.1 years ago by 20k
149
votes
35
replies
60k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 7 months ago by 40k • written 10.8 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 4 months ago by • 0 • written 5.3 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 7 months ago by 40k • written 10.5 years ago by 6.0k
288
votes
33
replies
99k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 7 months ago by 40k • written 9.9 years ago by 20k
13
votes
31
replies
5.8k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 6 months ago by 40k • written 4.1 years ago by 8.2k
84
votes
29
replies
30k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 9 weeks ago by • 0 • written 7.6 years ago by 20k
48
votes
28
replies
8.6k
views
9 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
4 months ago by Ram 40k
65
votes
26
replies
13k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 6 months ago by 40k • written 4.6 years ago by 16k
71
votes
26
replies
26k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 7 months ago by 40k • written 9.6 years ago by 98k
64
votes
26
replies
12k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 6 months ago by 40k • written 6.0 years ago by 86k
58
votes
25
replies
38k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 6 months ago by 40k • written 7.2 years ago by ★ 9.3k
95
votes
25
replies
32k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 7 months ago by 40k • written 11.0 years ago by 98k
9
votes
23
replies
9.1k
views
7 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 4 months ago by 40k • written 5.7 years ago by ▴ 310
18
votes
22
replies
8.1k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 8 days ago by ▴ 20 • written 3.8 years ago by 8.2k
86
votes
22
replies
80k
views
14 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 11 weeks ago by • 0 • written 5.2 years ago by ▴ 580
84
votes
21
replies
19k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 6 months ago by 40k • written 3.0 years ago by 3.0k
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 6 months ago by 40k • written 4.3 years ago by ★ 15k
53
votes
19
replies
42k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization bigwig chip-seq rna-seq
updated 7 months ago by 40k • written 11.5 years ago by 11k
8
votes
19
replies
12k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
mysql orthomcl
updated 6 months ago by 40k • written 8.9 years ago by ▴ 590
23
votes
19
replies
6.2k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
fastq mutation cancer target
updated 5 months ago by 40k • written 7.0 years ago by ★ 2.4k
42
votes
19
replies
7.4k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 7 months ago by 40k • written 10.6 years ago by 4.1k
47
votes
19
replies
13k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control fastqc
updated 8 months ago by 40k • written 10.6 years ago by 98k
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 7 months ago by 40k • written 9.9 years ago by 20k
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 4 months ago by 134k • written 9.9 years ago by 20k
12
votes
17
replies
2.5k
views
Tutorial: How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola bwa
updated 9 months ago by 40k • written 8.3 years ago by 98k
99
votes
16
replies
32k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 6 months ago by 40k • written 7.2 years ago by 26k
25
votes
15
replies
8.4k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
course training mooc
updated 7 months ago by 40k • written 10.7 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 6 months ago by 40k • written 7.0 years ago by ▴ 310
61
votes
15
replies
13k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 4 months ago by 40k • written 5.0 years ago by 16k
34
votes
15
replies
5.8k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 6 months ago by 40k • written 4.3 years ago by ★ 9.3k
7
votes
14
replies
3.0k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 11 months ago by • 0 • written 19 months ago by ▴ 30
30
votes
14
replies
16k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 7 months ago by 40k • written 10.7 years ago by 6.0k
75
votes
14
replies
15k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 7 months ago by 40k • written 10.4 years ago by 9.7k
50
votes
14
replies
75k
views
10 follow
Tutorial: Using R in Conda
R
updated 6 months ago by 40k • written 3.2 years ago by ▴ 750
20
votes
14
replies
3.6k
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 5 months ago by 40k • written 7.4 years ago by ▴ 460
75
votes
13
replies
66k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification
updated 11 months ago by 40k • written 9.9 years ago by ★ 1.2k
323 results • Page 1 of 7
Recent Votes
A: .gstmp extension on .bam files downloaded from google bucket; and EOF marker is
Comment: Significance testing of top vs. random SNPs
Answer: Search RCSB with a list of protein names?
A: running RAxML and MrBayes over concatinated multiple sequence alignments
Comment: Weirdness in annotation (missing allele frequencies)
Comment: Weirdness in annotation (missing allele frequencies)
Comment: ncbi error report log for validate fastq issue
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Recent Replies
Comment: Getting the overlap between two GTF files by Alex Reynolds 35k
What would that be?
Answer: Encountering Error while Running 'make vcf' in Biostar Handbook by Tully • 0
@ialbert ,I am deeply immersed in the fog and request the help ,please
Comment: bedtools intersect by position & stand not working even with common regions by rfran010 ▴ 830
are you sure bedtools can handle the non-standard location of strand information?
Answer: Getting the overlap between two GTF files by rfran010 ▴ 830
Maybe somebody knows something I don't, but I feel like bedtools should be able to handle your gtf files directly. If it's not done alre…
Answer: vcf.gz to vcf by Mark ★ 1.3k
As the error says, the file is not compressed. In linux the file extension is essentially optional. The file could be named `my.vcf.txt` ye…
Answer: Search RCSB with a list of protein names? by Jiyao Wang ▴ 340
You can use NCBI esearch to search the protein names against the structure database to get the PDB IDs, then retrieve the structures.
Answer: How to get ncol = nrow? by Mark ★ 1.3k
Without your actual data, it's hard to assist. I think what you're asking is 'how do I rename the rows of my dataframe(s)'. Taking the …
Comment: MAKER: WARNING: Could not get initialization lock. Trying Again... by GenoMax 134k
What kind of hardware are you running this on? You need to have the right kind of hardware (multiple CPU's not just cores), MPI libraries a…
Answer: Getting the overlap between two GTF files by Alex Reynolds 35k
Using `bedops --intersect` and `gtf2bed` will get their common genomic space: ``` bedops --intersect <(gtf2bed < transcripts.gtf) <(gtf2be…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook by Tully • 0
```bash # Obtain the makefile curl -s http://data.biostarhandbook.com/make/snpcall.mk > Makefile # Run the makefile make vcf ``` Error me…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook by Tully • 0
> System Information: Ubuntu 22.04 (WSL2) > > Shell: zsh > > Installation Verification: Yes, doctor.py OK [1]: https://www.biostarhand…
Comment: Retrieve The Reads And Fastq From Bam File by Reem • 0
Did it affect the bamtofastq output file? if so how did you solve the problem? Thanks
Answer: How to import bigwig files into igvR by Trivas ★ 1.5k
You could try seeing if this fixes your issue with rtracklayer: https://support.bioconductor.org/p/p133244/
Comment: Weirdness in annotation (missing allele frequencies) by Jeremy Leipzig 21k
0.60625 is 97/160 so if you have 80 individuals in your VCF that's an internal allele frequency, not gnomAD
Comment: Weirdness in annotation (missing allele frequencies) by Can Abdullah • 0
Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
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