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353 results • Page 2 of 8
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1
vote
0
replies
893
views
Tutorial: Slurm and parallelization
slurm
19 months ago by Juke34 7.5k
1
vote
0
replies
865
views
Tutorial: How to: make Camellia sinensis var. sinensis (black tea) custom annotation files for BINGO Cytoscape
bingo cytoscape
20 months ago by Pratik ▴ 850
12
votes
1
reply
1.8k
views
Tutorial: PCR Primer or Primer+Probe design
pcr probe rt-pcr qpcr primer
updated 20 months ago by ★ 14k • written 20 months ago by 84k
115
votes
66
replies
39k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera ENA fastq-dump Tutorial Fastq
7 months ago by ATpoint 68k
4
votes
0
replies
843
views
Tutorial: Long Read Genome Assembly Video Series
long-read genome-assembly
20 months ago by pbpanigrahi ▴ 420
0
votes
1
reply
694
views
Tutorial: Add Customized Filters in GDC
gdc
updated 20 months ago by 21k • written 20 months ago by ▴ 710
64
votes
26
replies
10k
views
11 follow
Tutorial: Generating consensus sequence from bam file
bam consensus fasta Tutorial
updated 20 months ago by ▴ 180 • written 3.9 years ago by 15k
12
votes
20
replies
11k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
seurat single cell RNA-Seq TCR Tutorial
20 months ago by jared.andrews07 ★ 14k
4
votes
2
replies
1.9k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle 5.0 Tutorial
updated 20 months ago by 125k • written 3.6 years ago by ★ 9.2k
45
votes
14
replies
52k
views
10 follow
Tutorial: Using R in Conda
R Tutorial
updated 12 weeks ago by ▴ 20 • written 2.5 years ago by ▴ 690
31
votes
9
replies
22k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda Tutorial
updated 8 months ago by • 0 • written 2.5 years ago by ▴ 140
98
votes
16
replies
29k
views
18 follow
Tutorial: Heatmaps in R
Tutorial R heatmap
8 months ago by Jean-Karim Heriche 26k
21
votes
2
replies
3.3k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 4 months ago by ▴ 40 • written 21 months ago by 7.5k
31
votes
6
replies
8.0k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
complexheatmap clustering arthritis pam Tutorial
17 months ago by Kevin Blighe 84k
78
votes
41
replies
27k
views
24 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 9 weeks ago by • 0 • written 9.3 years ago by ★ 7.6k
8
votes
0
replies
2.0k
views
Tutorial: Pipes in R: An introduction and some advanced tips and tricks.
R
22 months ago by rpolicastro 10k
234
votes
176
replies
83k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 3 months ago by 37k • written 7.5 years ago by ★ 4.6k
6
votes
0
replies
1.3k
views
Tutorial: data.frames in R: How vectorization can save you time and heartache
R
22 months ago by rpolicastro 10k
8
votes
1
reply
939
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
awk fasta Tutorial
22 months ago by Kevin Blighe 84k
17
votes
9
replies
4.2k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
R tidyverse gene Tutorial
updated 16 months ago by ★ 1.1k • written 2.4 years ago by 10k
12
votes
2
replies
976
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R Tutorial
22 months ago by rpolicastro 10k
146
votes
35
replies
57k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics Tutorial next-gen
updated 8 months ago by • 0 • written 10.2 years ago by ★ 1.6k
14
votes
2
replies
2.6k
views
Tutorial: Methylation Analysis Tutorial in R_part2
RNA-Seq R methylation Tutorial cancer
4 months ago by Hamid Ghaedi 2.8k
4
votes
0
replies
1.6k
views
Tutorial: Building mosdepth on macOS
mosdepth nim Tutorial
22 months ago by ATpoint 68k
16
votes
7
replies
12k
views
Tutorial: Integrating VDJ sequencing data with Seurat
Seurat clonotyping VDJ sc-RNAseq Tutorial
updated 23 months ago by 8.6k • written 3.6 years ago by ▴ 310
274
votes
33
replies
90k
views
24 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates tutorial Tutorial
updated 12 months ago by ▴ 100 • written 9.3 years ago by 20k
5
votes
0
replies
3.3k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap Tutorial
2.0 years ago by GenoMax 125k
10
votes
0
replies
4.1k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap Tutorial
2.0 years ago by GenoMax 125k
10
votes
0
replies
2.4k
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap Tutorial
2.0 years ago by GenoMax 125k
11
votes
1
reply
2.1k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq Tutorial
updated 14 months ago by 68k • written 2.1 years ago by ★ 22k
40
votes
9
replies
10k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell Tutorial flow-cytometry
9 weeks ago by Ahill ★ 1.9k
0
votes
1
reply
2.3k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
taxonomy python biosql Tutorial
updated 2.1 years ago by • 0 • written 4.5 years ago by ▴ 310
76
votes
13
replies
14k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 15 months ago by 37k • written 8.7 years ago by 19k
6
votes
10
replies
4.2k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
dna methylation Tutorial DMR
2.1 years ago by dec986 ▴ 340
41
votes
6
replies
11k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
maf vcf ensembl tcga somatic Tutorial
2.1 years ago by Cyriac Kandoth 5.8k
5
votes
2
replies
4.3k
views
Tutorial: bam2rpkm by bedtools
RNA-Seq bam rpkm bedtools Tutorial
updated 2.2 years ago by 68k • written 5.3 years ago by ▴ 130
16
votes
11
replies
7.2k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation Tutorial
5 months ago by Ram 37k
42
votes
33
replies
6.6k
views
8 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
meta how-to documentation Tutorial
2.2 years ago by Ram 37k
95
votes
6
replies
21k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
snakemake conda workflow Tutorial
updated 2.2 years ago by ▴ 50 • written 4.4 years ago by 15k
17
votes
40
replies
15k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
run easy orthomcl all-v-all mcl Tutorial
updated 2.2 years ago by ★ 2.0k • written 6.6 years ago by ▴ 160
23
votes
4
replies
5.9k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
enrichedheatmap chip-seq atac-seq heatmap Tutorial
updated 19 months ago by ★ 1.2k • written 3.5 years ago by 68k
13
votes
4
replies
4.0k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
R RNA-Seq Transcriptomics Tutorial bioconductor
12 months ago by Thind amarinder ▴ 280
26
votes
0
replies
2.0k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
variant interpretation annotation clinical cancer Tutorial
2.3 years ago by Malachi Griffith 19k
10
votes
1
reply
1.9k
views
Tutorial: introduce a tool for fast identification of SARS-CoV-2 and other microbes from sequencing data
COVID-19 fastv Tutorial SARS-CoV-2
2.3 years ago by chen ★ 2.4k
60
votes
52
replies
38k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
R plotly volcano plot Tutorial
updated 24 days ago by 37k • written 6.3 years ago by ★ 3.3k
10
votes
7
replies
4.2k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
STAR STARsolo 10x Chromium Tutorial
updated 13 months ago by 125k • written 2.4 years ago by 84k
18
votes
21
replies
6.6k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat Tutorial annotation
updated 6 weeks ago by ▴ 20 • written 3.2 years ago by 7.5k
0
votes
0
replies
798
views
Tutorial: BrainArray CDF, annotation, etc
brainarray cdf db Tutorial
2.4 years ago by Kevin Blighe 84k
12
votes
0
replies
2.0k
views
Tutorial: Long versus wide data for plotting genomics data in R.
R tidyverse ggplot2 Tutorial data.table
22 months ago by rpolicastro 10k
75
votes
70
replies
15k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment Tutorial david
updated 12 months ago by • 0 • written 5.0 years ago by 84k
353 results • Page 2 of 8
Recent Votes
C: Reorder heatmap rows in a dataset with missing values
A: Difference between GTF file with CHR and without CHR. ENSEMBL
Answer: Base recalibration in normal vs. tumor somatic variant calling in WXS data?
A: from .BAM to .BAI using samtools
Comment: bgzip error 4
Answer: Gene Set Enrichment Analysis, pathway, metabolism
Answer: Gene Set Enrichment Analysis, pathway, metabolism
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Popular Question to tianshenbio ▴ 160
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Recent Replies
Answer: trainGlimmerHMM Error while training a genome by congliu37 • 0
Hello, I got the same error using ~20,000 genes for training and it was solved by reducing training gene set. I assume GlimmerHMM was no…
Comment: How to Calulate Allele Frequency from a VCF File? by Jeremy Leipzig 21k
That's correct. You don't have biallelic alleles in mitochondria, so you can use either the Allele depth (AD) or depth of coverage (DP) for…
Comment: How to calculate tumor mutation burden (TMB)? by Fabio Marroni ★ 2.9k
I just published a [post][1] on my blog, in which I include a simple R function for computing TMB. Try to see if that helps. I followed the…
Comment: Gene Set Enrichment Analysis, pathway, metabolism by Rob ▴ 160
Thank you FrankStarling, ATpoint, jv, these were so helpful.
Comment: translate CDS to prot formatted with nt nubers by Pierre Lindenbaum 152k
> with nucleotide numbers and DNA/prot aligned line by line what does it mean ? Create a Minimal, Reproducible Example to enable others t…
Comment: How to translate CDS to an amino acid sequence by vvasta • 0
I tried several of the online DNA translation tools but have not found one that would output DNA/prot alignment with nucleotide number w…
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb? by Pierre Lindenbaum 152k
but you already knew it. https://www.biostars.org/p/9551097/#9551098
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb? by Pierre Lindenbaum 152k
your question is not related to bioinformatics. Ask stackoverflow.com.
Comment: Statistical test for checking cis regulation? by Fabio Marroni ★ 2.9k
Hi lumos. It is not very clear to me what kind of information are you using for the test and how are you measuring cis-regulation. Are you …
Comment: Error 134 while aligning using hisat2 by Fabio Marroni ★ 2.9k
Other instances of the same error were indeed related to disk [space][1]. Can you post the output of the command: `df -h /bams/`? Another p…
Comment: **Error: unable to open file or unable to determine types for file** by Pierre Lindenbaum 152k
``` Please ensure that your file is TAB delimited (e.g., cat -t FILE). - Also ensure that your file has integer chromosome coordinates in t…
Comment: bgzip error 4 by Pierre Lindenbaum 152k
I/O error. Where are you writing , which filesytem ? do you have enough space ? what is the output of gzip < chr1.vcf.gz > chr1.vcf.gz…
Comment: Error: unable to open file or unable to determine types for file bed file by Neel ▴ 10
**Error: unable to open file or unable to determine types for file** Hi i am trying to run this commands **bedtools intersect -a Ec_k1…
Answer: Anti-miRNA oligonuclotide identification by Asan Emirsale • 0
You should find complementary sequences to make the miRNA silent. Should it be the Biopython or another tool. The solution might be as simp…
Comment: counting reads in a fastq file using a refrence fasta file by vaslanzadeh ▴ 10
Thanks, this works but it is extremely slow, is there any other alternatives?
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