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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
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
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 10.6 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
76
votes
13
replies
15k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 23 months ago by 40k • written 9.3 years ago by 19k
15
votes
5
replies
15k
views
Tutorial: How to create a mutation lolliplot with GenVisR
bioconductor graphics R genvisr
updated 5 months ago by 40k • written 7.3 years ago by 20k
54
votes
5
replies
14k
views
6 follow
Tutorial: Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
r
updated 12 months ago by 40k • written 9.8 years ago by ★ 1.2k
16
votes
7
replies
14k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 6 months ago by 40k • written 4.3 years ago by ▴ 310
16
votes
11
replies
14k
views
7 follow
Tutorial: retrieve full TCGA datasets from cBioportal with R
TCGA RNA-seq data-retrieval cBioportal R
updated 6 months ago by 40k • written 6.9 years ago by ★ 4.7k
11
votes
7
replies
14k
views
Tutorial: Removing rows with duplicate values based on 1 or more key values - linux awk
awk linux bash
updated 4 months ago by 40k • written 6.0 years ago by 86k
20
votes
4
replies
14k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix
updated 7 months ago by 40k • written 10.5 years ago by 20k
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
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
19
votes
3
replies
13k
views
Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 14 months ago by 40k • written 7.6 years ago by ★ 9.3k
64
votes
13
replies
13k
views
11 follow
Tutorial: Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.
muTect GATK Picard Exome
updated 19 months ago by 40k • written 8.9 years ago by ★ 2.4k
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
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
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
16
votes
0
replies
12k
views
Tutorial: Workshop - Analysis Of Next Generation Sequencing Data
RNA-seq
updated 7 months ago by 40k • written 11.5 years ago by 10k
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
44
votes
3
replies
12k
views
Tutorial: A Wet-Lab Guide to 'what I wish I had known' for Computational Biology
bioinformatics computational-biology
updated 5 months ago by 40k • written 7.5 years ago by ★ 3.2k
15
votes
5
replies
12k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 6 months ago by 40k • written 5.8 years ago by ▴ 760
43
votes
6
replies
12k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 6 months ago by 40k • written 9.7 years ago by 6.0k
39
votes
8
replies
11k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 6 months ago by 40k • written 3.0 years ago by 3.0k
7
votes
2
replies
11k
views
Tutorial: Howto use NCBI programs behind a HTTP proxy
blast-plus HTTP-proxy SRA-toolkit
updated 14 months ago by 40k • written 7.6 years ago by ★ 1.8k
4
votes
13
replies
11k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 3 months ago by 40k • written 4.6 years ago by ▴ 140
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 6 months ago by 40k • written 9.5 years ago by ★ 1.9k
49
votes
7
replies
11k
views
7 follow
Tutorial: Genome Assembly Review Papers
assembly papers
updated 7 months ago by 40k • written 11.1 years ago by 98k
13
votes
3
replies
11k
views
Tutorial: Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome plot coverage samtools
updated 5 weeks ago by ▴ 20 • written 6.5 years ago by ★ 1.6k
0
votes
0
replies
11k
views
Tutorial: Using PatMatch to search for nucleic and protein sequence patterns and integrate the results with Python/Jupyter for downstream analysis
Jupyter Python pattern
20 months ago by Wayne ★ 1.8k
28
votes
13
replies
11k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 20 months ago by ★ 1.2k • written 23 months ago by 98k
70
votes
5
replies
11k
views
8 follow
Tutorial: Bioinformatics For Metagenomic Analyses
QC taxonomy metagenomics
updated 18 months ago by 40k • written 9.5 years ago by ★ 1.8k
31
votes
6
replies
11k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 6 months ago by 40k • written 3.4 years ago by 86k
31
votes
8
replies
10k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
python pipeline
updated 6 months ago by 40k • written 9.5 years ago by ▴ 810
8
votes
9
replies
10k
views
Tutorial: Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs (ONE-LINERS)
fastq fasta
updated 6 months ago by 40k • written 9.5 years ago by ★ 1.8k
10
votes
4
replies
10k
views
Tutorial: Using the MinION MinKNOW software on Ubuntu 1604
long-reads oxford-nanopore minion
updated 6 months ago by 40k • written 4.2 years ago by 5.5k
18
votes
2
replies
9.7k
views
Tutorial: Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq Galaxy IGB
updated 18 months ago by 40k • written 8.9 years ago by ▴ 860
14
votes
0
replies
9.2k
views
Tutorial: How to generate PCA plot and heatmaps in R
heatmap PCA RNA-Seq R
updated 5 months ago by 40k • written 7.0 years ago by ★ 3.4k
61
votes
6
replies
9.2k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 7 months ago by 40k • written 10.1 years ago by 9.7k
11
votes
7
replies
9.1k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 4 months ago by 40k • written 2.6 years ago by ▴ 350
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
16
votes
5
replies
8.7k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
api perl biomart
updated 7 months ago by 40k • written 11.0 years ago by 20k
19
votes
4
replies
8.6k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 7 months ago by 40k • written 10.6 years ago by 98k
20
votes
0
replies
8.5k
views
Tutorial: Metagenomics Review Papers
metagenomics papers
updated 7 months ago by 40k • written 11.1 years ago by 98k
48
votes
28
replies
8.5k
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
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
9
votes
0
replies
8.4k
views
Tutorial: Installing And Running Ncbi Blast
blast
updated 7 months ago by 40k • written 11.5 years ago by ▴ 540
20
votes
4
replies
8.4k
views
Tutorial: DE analysis by edgeR
RNA-Seq R edgeR
updated 5 months ago by 40k • written 7.0 years ago by ★ 4.2k
10
votes
1
reply
8.3k
views
Tutorial: How to select reads with specific flag using samtools
next-gen-sequencing
updated 4 months ago by 40k • written 6.1 years ago by ▴ 110
3
votes
3
replies
8.3k
views
Tutorial: High Speed Downloading of SRA, SAM and Fastq Files
fastq sam Aspera-Connect sra
updated 4 months ago by 40k • written 5.8 years ago by ▴ 100
379 results • Page 2 of 8
Recent Votes
How to assign read groups to bam files?
C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
Answer: Which function is best for pathway analysis?
Comment: Hisat2 index and alignment question
Answer: Low Alignment rate
Answer: Unable to build applet in DNAnexus, .jar file not found
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Popular Question to bharata1803 ▴ 550
Teacher to GenoMax 134k
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Recent Replies
Comment: Which function is best for pathway analysis? by luffy ▴ 40
@chris Please look into @Hamid Ghaedi's well documented [post][1] on ORA and GSEA, Or [this][2] documentation. Hope this helps. [1]: ht…
Comment: Bacterial Pangenome Analysis by kirankumareripogu ▴ 10
Hi @liorglic, Thank you for your prompt response. I totally agree with you that different blastp cuttoffs provide different results and…
Answer: Fetch Fastq files directly for SRA data by Rob 6.2k
What is the accession for the project? Many — though not all — of the projects present in the NCBI SRA are also hosted in the European Nuc…
Comment: Dataset's name in BioMart for S. pombe by YUYANG.OON • 0
Works with `useMart(biomart="fungi_mart", dataset="spombe_eg_gene", host="https://fungi.ensembl.org")`
Comment: Bug of vg surject by Jordan M Eizenga ▴ 360
This is still hard to interpret without the commands. What would help is if you literally copied the full UNIX commands along with their re…
Comment: Which function is best for pathway analysis? by Chris ▴ 180
Thank you for your reply! Do you have code that I and others can implement? I am not sure how to customize the gmt file from my differentia…
Comment: Bug of vg surject by Qi • 0
Thanks your reply! my resulte show below: 5x_pan_sv.bam 1347587601 #converted from gam to bam F1 indel=0.830392 snp=0.932511 5…
Comment: Bug of vg surject by Jordan M Eizenga ▴ 360
It might help us to diagnose the problem if you included the exact commands that you used and showed the results that you are concerned abo…
Answer: Which function is best for pathway analysis? by Yogi ▴ 20
Few things to mention. Pathway Enrichment Analysis can be split into two categories. 1. Functional Class Scoring Methods 2. Overrepr…
Answer: identify DEGs across all conditions and per specific conditions by Yogi ▴ 20
Couple of things. (Feel free to correct if I'm misunderstanding). "DESeq2" is meant for 1v1 comparisons. If you're trying to compar…
Comment: Hisat2 index and alignment question by Istvan Albert 98k
yes correct you have to pass the full prefix and not the directory
Comment: Low Alignment rate by dsull ★ 4.7k
Wow! Didn't realize the repeat-masked file could have such a large influence on alignment. Very good to know -- I guess I'll need to dive i…
Comment: Troubles launch IGV on Linux(Debian) by morovatunc ▴ 550
Disclaimer: My comment could be totally unrelated. I would give these a try if you have noone comment/answer your problem. I have had this…
Comment: How to check RNAseq support for annotated genes? by Michael 53k
> I tried it using STAR to map the transcript to the annotation gtf file That is not what STAR is for. STAR is for aligning short reads in…
Comment: Low Alignment rate by Mehwish • 0
Thanks alot! This worked out for me https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz …
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