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325 results • Page 2 of 7
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16
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11
replies
14k
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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
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 8.8 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
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
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 3.3 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 9.4 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
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 6 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
2
votes
2
replies
8.2k
views
Tutorial: Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ UMI fastp
updated 4 months ago by 40k • written 5.8 years ago by ★ 2.4k
81
votes
8
replies
8.1k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop lectures genomics training
updated 6 months ago by 40k • written 9.3 years ago by 19k
18
votes
22
replies
8.0k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 2 days ago by ▴ 20 • written 3.8 years ago by 8.2k
12
votes
5
replies
7.9k
views
Tutorial: How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 5 months ago by 40k • written 7.3 years ago by ★ 9.3k
0
votes
0
replies
7.8k
views
Tutorial: Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R eviews
updated 4 months ago by 40k • written 5.7 years ago by ▴ 10
16
votes
11
replies
7.7k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
6 months ago by Ram 40k
6
votes
1
reply
7.7k
views
Tutorial: Expression Analysis Of Rna-Seq Experiments With Tophat And Cufflinks
tophat RNA-seq cufflinks
updated 7 months ago by 40k • written 11.4 years ago by 98k
20
votes
2
replies
7.6k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 4 months ago by 40k • written 5.8 years ago by ★ 3.4k
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
50
votes
1
reply
7.4k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 7 months ago by 40k • written 3.0 years ago by 76k
6
votes
4
replies
7.2k
views
Tutorial: Overlay Multiple Tracks In Ucsc Browser [Quick Minimal Tutorial]
visualization ChIP-seq RNA-seq ucsc-genome-browser bigwig
updated 7 months ago by 40k • written 10.5 years ago by 11k
60
votes
2
replies
7.1k
views
Tutorial: Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 7 months ago by 40k • written 11.1 years ago by 98k
32
votes
4
replies
7.0k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 6 months ago by 40k • written 4.9 years ago by ★ 1.6k
4
votes
2
replies
7.0k
views
Tutorial: Analyzing Genomewide Association Study Data: A Tutorial Using Plink
plink gwas
updated 7 months ago by 40k • written 11.3 years ago by 98k
64
votes
5
replies
7.0k
views
10 follow
Tutorial: Informatics of RNA-Seq.
next-gen RNA-Seq
updated 11 months ago by 40k • written 8.1 years ago by 12k
325 results • Page 2 of 7
Recent Votes
Comment: Assistance with Fungal Genome Annotation Using Maker and BLAST
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
Comment: Hisat2 index and alignment question
Comment: Dotplot error: subscript out of bound
Comment: Dotplot : how to self-define the range of legend
Answer: Dotplot : how to self-define the range of legend
Convert SAM to BAM
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Recent Replies
Comment: Assistance with Fungal Genome Annotation Using Maker and BLAST by Edoardo • 0
I have 13,576 proteins in my file. I tried on a small set of 3 proteins and it worked fine!
Comment: Assistance with Fungal Genome Annotation Using Maker and BLAST by Mensur Dlakic ★ 24k
It should be faster, though you are not telling us how many proteins are in your query file. I suggest you use as many threads as availabl…
Comment: Hisat2 index and alignment question by Athena • 0
That worked! Thank you. Didn't know that was an option... now I know.
Comment: Assistance with Fungal Genome Annotation Using Maker and BLAST by Edoardo • 0
I ran blastp with the following command: blastp \ -db /path/to/Annotation_db/uniprot_fungi.fasta \ -query MYGEN.maker.output/…
Comment: Hisat2 index and alignment question by Athena • 0
Pathway of my reference genome ![reference index pathway][1] when I tried running this command `hisat2 -p 8 -x /path/to/musculus_index…
Comment: Dotplot : how to self-define the range of legend by Xuhao • 0
Thanks for your kind help.
Comment: Dotplot : how to self-define the range of legend by zau saa ▴ 50
add `breaks = c(-1, -0.5, 0, 0.5, 1)` to `scale_colour_gradientn()`
Comment: Dotplot : how to self-define the range of legend by Xuhao • 0
It works!!! Thanks so much. Can I ask one more question? How to change the "average expression" scale into "-1, -0.5, 0, 0.5, 1"?
Comment: Low Alignment rate by dsull ★ 4.7k
Did you run FASTQC to check the quality of your sequencing samples? Otherwise, try taking some the reads that failed to align, and run the…
Comment: Integrated Seurat object change name of the two conditions by Amitm ★ 2.2k
Hi, See this [prev. post][1] where I contributed to, on accessing the meta data slot in a seurat object. There is more than one way. [1…
Comment: scRNAseq Differential expression analysis by jared.andrews07 ★ 15k
I appreciate this statement and it largely mirrors my own. Lior sometimes makes extremely salient and important points. Other times, he's t…
Comment: Highly inflated p-values in GWAS by regenie by cwwong13 ▴ 20
Thanks @4galaxy77 . The first 10 PCs were included in the calculation of the trait residuals, but still results were highly inflated.
Comment: Hisat2 index and alignment question by Istvan Albert 98k
the most logical and simple explanation is that most likely the path to index is specified incorrectly show us the paths with say `ls` the…
Comment: How to change from gene_id to GeneID/EntrezID using R by Kevin Blighe 86k
It would have been good if you had mentioned the species in your opening question. Regarding the fact that it may not be related to Ensembl…
Comment: How to change from gene_id to GeneID/EntrezID using R by Nicolas • 0
Thank you for your help but my data are not related to ENSMBL and im not working with any model organism that allow me to use the org packa…
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