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231 results • Page 2 of 5
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16
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11
replies
13k
views
7 follow
Tutorial: retrieve full TCGA datasets from cBioportal with R
TCGA RNA-seq data-retrieval cBioportal R
updated 15 days ago by 38k • written 6.4 years ago by ★ 4.6k
20
votes
4
replies
13k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix
updated 4 weeks ago by 38k • written 10.0 years ago by 20k
16
votes
7
replies
12k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 15 days ago by 38k • written 3.8 years ago by ▴ 310
47
votes
19
replies
12k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control fastqc
updated 11 weeks ago by 38k • written 10.1 years ago by 97k
16
votes
0
replies
12k
views
Tutorial: Workshop - Analysis Of Next Generation Sequencing Data
RNA-seq
updated 5 weeks ago by 38k • written 11.0 years ago by 9.9k
8
votes
19
replies
12k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
mysql orthomcl
updated 20 days ago by 38k • written 8.4 years ago by ▴ 580
12
votes
20
replies
11k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 15 days ago by 38k • written 3.8 years ago by ★ 14k
64
votes
26
replies
11k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 15 days ago by 38k • written 5.5 years ago by 84k
17
votes
3
replies
11k
views
Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 8 months ago by 38k • written 7.1 years ago by ★ 9.3k
43
votes
6
replies
11k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 27 days ago by 38k • written 9.2 years ago by 5.9k
7
votes
2
replies
11k
views
Tutorial: Howto use NCBI programs behind a HTTP proxy
blast-plus HTTP-proxy SRA-toolkit
updated 8 months ago by 38k • written 7.1 years ago by ★ 1.8k
15
votes
5
replies
11k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 20 days ago by 38k • written 5.3 years ago by ▴ 740
64
votes
26
replies
11k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 16 days ago by 38k • written 4.1 years ago by 16k
48
votes
7
replies
11k
views
7 follow
Tutorial: Genome Assembly Review Papers
assembly papers
updated 5 weeks ago by 38k • written 10.6 years ago by 97k
40
votes
9
replies
10k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 23 days ago by 38k • written 9.0 years ago by ★ 1.9k
70
votes
5
replies
10k
views
8 follow
Tutorial: Bioinformatics For Metagenomic Analyses
QC taxonomy metagenomics
updated 11 months ago by 38k • written 9.0 years ago by ★ 1.8k
30
votes
8
replies
10k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
python pipeline
updated 23 days ago by 38k • written 9.0 years ago by ▴ 800
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 23 days ago by 38k • written 9.0 years ago by ★ 1.8k
3
votes
13
replies
9.4k
views
Tutorial: Merging multiple vcf files into Single vcf file
merge vcf bcftools
updated 20 days ago by 38k • written 4.1 years ago by ▴ 140
37
votes
8
replies
9.3k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 20 days ago by 38k • written 2.5 years ago by 2.9k
9
votes
4
replies
9.0k
views
Tutorial: Using the MinION MinKNOW software on Ubuntu 1604
long-reads oxford-nanopore minion
updated 15 days ago by 38k • written 3.7 years ago by 4.6k
60
votes
6
replies
8.9k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 4 weeks ago by 38k • written 9.6 years ago by 9.5k
31
votes
6
replies
8.7k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 15 days ago by 38k • written 2.9 years ago by 84k
19
votes
4
replies
8.4k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 4 weeks ago by 38k • written 10.1 years ago by 97k
16
votes
5
replies
8.4k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
api perl biomart
updated 5 weeks ago by 38k • written 10.5 years ago by 20k
20
votes
0
replies
8.4k
views
Tutorial: Metagenomics Review Papers
metagenomics papers
updated 5 weeks ago by 38k • written 10.6 years ago by 97k
9
votes
0
replies
8.1k
views
Tutorial: Installing And Running Ncbi Blast
blast
updated 5 weeks ago by 38k • written 11.0 years ago by ▴ 540
24
votes
15
replies
7.9k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
course training mooc
updated 4 weeks ago by 38k • written 10.2 years ago by 9.5k
81
votes
8
replies
7.8k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop lectures genomics training
updated 23 days ago by 38k • written 8.8 years ago by 19k
6
votes
1
reply
7.6k
views
Tutorial: Expression Analysis Of Rna-Seq Experiments With Tophat And Cufflinks
tophat RNA-seq cufflinks
updated 5 weeks ago by 38k • written 10.9 years ago by 97k
16
votes
11
replies
7.3k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
15 days ago by Ram 38k
12
votes
0
replies
7.3k
views
Tutorial: Plot average methylation levels across TSS region
bedtools RRBS R methylation
updated 11 months ago by 38k • written 8.2 years ago by ★ 4.6k
42
votes
19
replies
7.1k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 4 weeks ago by 38k • written 10.1 years ago by 4.1k
18
votes
22
replies
7.1k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 15 days ago by 38k • written 3.3 years ago by 7.8k
6
votes
4
replies
6.9k
views
Tutorial: Overlay Multiple Tracks In Ucsc Browser [Quick Minimal Tutorial]
visualization ChIP-seq RNA-seq ucsc-genome-browser bigwig
updated 4 weeks ago by 38k • written 10.0 years ago by 11k
60
votes
2
replies
6.9k
views
Tutorial: Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 5 weeks ago by 38k • written 10.6 years ago by 97k
4
votes
2
replies
6.8k
views
Tutorial: Analyzing Genomewide Association Study Data: A Tutorial Using Plink
plink gwas
updated 5 weeks ago by 38k • written 10.9 years ago by 97k
42
votes
33
replies
6.8k
views
8 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
meta how-to documentation
15 days ago by Ram 38k
64
votes
5
replies
6.7k
views
10 follow
Tutorial: Informatics of RNA-Seq.
next-gen RNA-Seq
updated 5 months ago by 38k • written 7.6 years ago by 12k
26
votes
17
replies
6.7k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv
updated 6 months ago by 38k • written 8.6 years ago by 5.9k
15
votes
2
replies
6.5k
views
Tutorial: Genotype And Snp Calling Review Papers
snp
updated 5 weeks ago by 38k • written 10.6 years ago by 97k
32
votes
4
replies
6.4k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 12 days ago by 38k • written 4.4 years ago by ★ 1.5k
15
votes
0
replies
6.3k
views
Tutorial: Introduction To Ngs Bioinformatics By The Bioinformatics Team At The University Of Texas
course training
updated 5 weeks ago by 38k • written 10.8 years ago by 97k
23
votes
4
replies
6.2k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 15 days ago by 38k • written 3.6 years ago by 70k
44
votes
1
reply
6.2k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 6 weeks ago by 38k • written 2.5 years ago by 70k
14
votes
2
replies
6.1k
views
Tutorial: ChIP-seq analysis tutorial
Tutorials ChIP-Seq
updated 6 months ago by 38k • written 7.6 years ago by ★ 2.9k
9
votes
7
replies
6.1k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
Software clusterProfiler Tool rna-seq tool
updated 6 months ago by • 0 • written 2.1 years ago by ▴ 240
19
votes
9
replies
6.0k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 4 weeks ago by 38k • written 9.8 years ago by 9.5k
6
votes
0
replies
5.9k
views
Tutorial: Leveraging Flow Order And Flow Signals From Ion Torrent Data
ion-torrent
updated 5 weeks ago by 38k • written 10.9 years ago by ▴ 360
29
votes
5
replies
5.9k
views
Tutorial: Gnu Parallel Tutorial
parallel gnu-parallel
updated 29 days ago by 38k • written 9.5 years ago by ★ 4.3k
231 results • Page 2 of 5
Recent Votes
Answer: Somatic truth set
Comment: Best way to visualize .paf or .sam alignment to a fasta file
Comment: Why not use ONLY promoter-bound peaks when testing for enrichment in differentia
Comment: Why not use ONLY promoter-bound peaks when testing for enrichment in differentia
Answer: What is the NCBI's definition of an "atypical genome"?
Answer: Variant caller reports a homozygous variant genotype, but more reads are associa
Any tips in landing a bioinformatic job?
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Recent Replies
Comment: Kallisto bustools for scRNA-seq by dsull ★ 4.0k
I have no idea what that is besides a bunch of jumbled sequences. You'll need look up the structure of the reads / library from wherever yo…
Comment: Aberrant splicing in bulk RNAseq by dsull ★ 4.0k
First thing: kallisto cannot interface with UMI-tools (kallisto doesn't use read headers and therefore you're stuck with "the kallisto way"…
Comment: Using Copy Number Alterations detected in other studies for the same tumor cell by lethalfang ▴ 90
There is some somatic SV study on these HCC1395: https://doi.org/10.1186/s13059-022-02816-6. There is also a CNA preprint from years ago b…
Comment: Somatic truth set by lethalfang ▴ 90
Just in case things are hard to find, for the WGS/WES, these are the data (what the file names mean: https://sites.google.com/view/seqc2/ho…
Comment: How to get subset of a Seurat object based on metadata? by jv ★ 1.0k
Hmm, not sure why `subset` doesn't match to '0:CD8 T cell' but maybe it's the ":"? An alternative option is the following: ``` idx <- whi…
Comment: GO enrichment analysis by Jeremy ▴ 770
g:Profiler has an Arabidopsis option: [g:Profiler][1] [1]: https://biit.cs.ut.ee/gprofiler/gost
Answer: Any tips in landing a bioinformatic job? by Carambakaracho ★ 3.2k
The first job is a nightmare and you will need some luck. I understand you're looking for an industry offering. Unfortunately I've worked o…
Comment: Best way to visualize .paf or .sam alignment to a fasta file by GenoMax 127k
Why not use IGV with SAM file? If you want a text based viewer then ASCIIGenome: https://asciigenome.readthedocs.io/en/latest/
Answer: What is the NCBI's definition of an "atypical genome"? by MirianT_NCBI ▴ 490
Hi, You can find more information about what constitute an [atypical genome in this FAQ][1]. Here's the list of reasons for a genome to …
Comment: How to get subset of a Seurat object based on metadata? by sunyeping ▴ 80
> skin$predicted_cell_type Error in rep.int(x = colnames(x = x), times = length(x = i)) : unimplemented type 'NULL' in 'rep3…
Comment: using CITE-seq data to cluster single cells by chi.delta ▴ 40
Let's say that based on known FACS data, I already know that three populations exist based on the two antibodies staining: single positive …
Answer: syntax errors when running part3 all-against-all by Adrian Altenhoff ★ 1.0k
Dear Sofia, this looks like the all-vs-all file is corrupted. maybe a race condition of to processes that tried to write the same file. …
Answer: Any tips in landing a bioinformatic job? by zhousun21 ▴ 40
Since you are just starting out, I suggest sending your resume to a few recruiters who specialize in science placements. They will intervie…
Comment: How to get subset of a Seurat object based on metadata? by jv ★ 1.0k
Do you have cells labeled "0:CD8 T Cell" in `skin$predicted_cell_type`?
Comment: using CITE-seq data to cluster single cells by ATpoint 70k
Think about it, how would any clustering with only two genes/features be informative? Is this really what you need? If you break it down, f…
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