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411 results • Page 3 of 9
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20
votes
6
replies
5.6k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 13 months ago by 43k • written 7.6 years ago by ★ 5.2k
20
votes
0
replies
8.7k
views
Tutorial: Metagenomics Review Papers
metagenomics papers
updated 14 months ago by 43k • written 11.7 years ago by 100k
20
votes
4
replies
14k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix
updated 14 months ago by 43k • written 11.1 years ago by 20k
19
votes
4
replies
8.9k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 14 months ago by 43k • written 11.1 years ago by 100k
19
votes
3
replies
14k
views
Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 21 months ago by 43k • written 8.2 years ago by ★ 9.4k
19
votes
7
replies
6.5k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 9 months ago by 82k • written 4.1 years ago by 6.4k
18
votes
13
replies
2.2k
views
Tutorial: Screen shots of text (please don't)!
meta
updated 11 months ago by 43k • written 7.1 years ago by 54k
18
votes
2
replies
10.0k
views
Tutorial: Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq Galaxy IGB
updated 2.1 years ago by 43k • written 9.5 years ago by ▴ 860
18
votes
2
replies
5.9k
views
Tutorial: Update kraken databases
database kraken k-mer python
updated 11 months ago by 43k • written 7.0 years ago by 5.3k
18
votes
40
replies
18k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 3.8 years ago by • 0 • written 7.8 years ago by ▴ 170
17
votes
0
replies
6.6k
views
Tutorial: Introduction To Ngs Bioinformatics By The Bioinformatics Team At The University Of Texas
course training
updated 14 months ago by 43k • written 11.8 years ago by 100k
17
votes
0
replies
13k
views
Tutorial: Workshop - Analysis Of Next Generation Sequencing Data
RNA-seq
updated 14 months ago by 43k • written 12.0 years ago by 11k
16
votes
6
replies
6.4k
views
Tutorial: How to make your snakefiles self-documenting
snakemake
updated 12 months ago by 43k • written 7.5 years ago by ★ 1.7k
16
votes
7
replies
16k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 13 months ago by 43k • written 4.9 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 13 months ago by 43k • written 7.5 years ago by ★ 4.7k
16
votes
5
replies
9.0k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
api perl biomart
updated 14 months ago by 43k • written 11.6 years ago by 20k
16
votes
5
replies
13k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 13 months ago by 43k • written 6.4 years ago by ▴ 800
16
votes
11
replies
8.2k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
13 months ago by Ram 43k
16
votes
3
replies
4.3k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 3.1 years ago by • 0 • written 3.6 years ago by 3.2k
16
votes
9
replies
7.0k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 22 months ago by ▴ 70 • written 2.4 years ago by ★ 1.3k
16
votes
3
replies
4.7k
views
Tutorial: NCBI blast tutorial
ncbi blast
updated 12 months ago by 43k • written 8.0 years ago by 11k
15
votes
7
replies
6.4k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 13 months ago by 43k • written 7.9 years ago by ★ 3.5k
15
votes
5
replies
15k
views
Tutorial: How to create a mutation lolliplot with GenVisR
bioconductor graphics R genvisr
updated 12 months ago by 43k • written 7.9 years ago by 20k
15
votes
1
reply
3.2k
views
Tutorial: Current Topics in Genome Analysis 2016 (collection of educational lectures)
genomics training lectures workshop
updated 12 months ago by 43k • written 8.0 years ago by 19k
15
votes
2
replies
6.9k
views
Tutorial: Genotype And Snp Calling Review Papers
snp
updated 14 months ago by 43k • written 11.7 years ago by 100k
15
votes
2
replies
3.0k
views
Tutorial: Introduction to bedtools.
bedtools
updated 13 months ago by 43k • written 9.4 years ago by 12k
15
votes
1
reply
4.0k
views
Tutorial: Dealing with nanopore fast5 files compressed with vbz
hdf5 nanopore fast5 vbz MinKNOW
updated 20 months ago by ★ 1.8k • written 2.3 years ago by 14k
15
votes
1
reply
7.1k
views
Tutorial: A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl SAM blast BED
updated 11 months ago by 43k • written 6.4 years ago by ★ 3.0k
15
votes
2
replies
2.1k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 18 months ago by ▴ 830 • written 2.6 years ago by ▴ 300
15
votes
4
replies
4.6k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 13 months ago by 43k • written 3.7 years ago by ▴ 340
14
votes
0
replies
8.3k
views
Tutorial: Video: ChIP-Seq Analysis and Visualization using Galaxy and IGB.
IGB ChIP-Seq Galaxy MACS RNA-Seq
updated 2.1 years ago by 43k • written 9.3 years ago by ▴ 860
14
votes
2
replies
6.5k
views
Tutorial: ChIP-seq analysis tutorial
ChIP-Seq
updated 13 months ago by 43k • written 8.6 years ago by ★ 3.9k
14
votes
0
replies
9.5k
views
Tutorial: How to generate PCA plot and heatmaps in R
heatmap PCA RNA-Seq R
updated 12 months ago by 43k • written 7.6 years ago by ★ 3.9k
14
votes
3
replies
20k
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 8 months ago by ▴ 30 • written 7.1 years ago by ★ 1.6k
14
votes
1
reply
3.1k
views
Tutorial: PCR Primer or Primer+Probe design
pcr probe rt-pcr qpcr primer
updated 2.9 years ago by ★ 16k • written 2.9 years ago by 87k
14
votes
31
replies
6.8k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 13 months ago by 43k • written 4.7 years ago by 8.5k
14
votes
2
replies
2.4k
views
Tutorial: Exploring OpenSNP - an RMarkdown report on crowdsourced genotypes and phenotypes
SNP R
updated 12 months ago by 43k • written 8.1 years ago by 22k
13
votes
3
replies
5.1k
views
Tutorial: Video: Visualization of whole genome DNA methylation data in IGB
Bismark BS-Seq RNA-Seq IGB
updated 23 months ago by 43k • written 9.1 years ago by ▴ 860
13
votes
6
replies
6.0k
views
Tutorial: Trim & align paired-end reads in a single pass
align trim fastq pipe paired-end
updated 12 months ago by 43k • written 7.9 years ago by 14k
13
votes
7
replies
6.2k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 13 months ago by 43k • written 3.6 years ago by 87k
12
votes
17
replies
3.0k
views
Tutorial: How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola bwa
updated 16 months ago by 43k • written 8.9 years ago by 100k
12
votes
0
replies
2.7k
views
Tutorial: Long versus wide data for plotting genomics data in R.
ggplot2 tidyverse data.table R
updated 13 months ago by 43k • written 3.7 years ago by 13k
12
votes
11
replies
7.5k
views
Tutorial: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI Bioproject SRA BioSample
updated 11 months ago by 43k • written 7.1 years ago by ★ 2.4k
12
votes
6
replies
5.0k
views
Tutorial: sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 21 months ago by 43k • written 8.2 years ago by ★ 4.3k
12
votes
1
reply
5.0k
views
Tutorial: RepSeq data processing and analysis
immunology tcr repseq sequencing repertoire
updated 18 months ago by 43k • written 8.7 years ago by 3.5k
12
votes
4
replies
2.2k
views
Tutorial: Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR DESeq2
updated 13 months ago by 43k • written 6.6 years ago by ▴ 590
12
votes
5
replies
2.4k
views
Tutorial: FASTA file split
fasta
updated 13 months ago by 43k • written 3.9 years ago by 8.5k
12
votes
0
replies
7.9k
views
Tutorial: Plot average methylation levels across TSS region
bedtools RRBS R methylation
updated 2.0 years ago by 43k • written 9.2 years ago by ★ 4.7k
12
votes
4
replies
5.4k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 14 months ago by 43k • written 3.2 years ago by ▴ 130
12
votes
20
replies
14k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 13 months ago by 43k • written 4.9 years ago by ★ 16k
411 results • Page 3 of 9
Recent Votes
Answer: How do I get the 3bp sequence on either side of a co-ordinate
What is the difference between HaplotypeCaller and UnifiedGenotyper?
What is the difference between HaplotypeCaller and UnifiedGenotyper?
RSeQC Output from infer_experiment.py - what does it mean?
ScRNAseq-How to correctly choose cell type marker genes
ScRNA data question
Comment: SRA to BAM
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Recent Replies
Answer: why renaming Idents in Seurat object doesn't work? by Bioinfotec ▴ 10
I think when you give indent to seuObj : Idents(seuObj) <- 'RNA_snn_res.0.1' You may wrongly assign other value to it such as …
Answer: ScRNAseq-How to correctly choose cell type marker genes by Bioinfotec ▴ 10
In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. F…
Answer: ScRNA data question by Bioinfotec ▴ 10
In violin plot, a dot represents a cell. Actually, the straight lines you see in your infected image just means these cells have the same e…
Comment: Sequence read length shorter than flow cell specification by GenoMax 141k
> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended If they sent data that is not what you…
Comment: How to know synonymous and non-synonymous SNPs from transcriptome sequencing by rohitsatyam102 ▴ 840
I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K). | …
Answer: Sequence read length shorter than flow cell specification by ATpoint 82k
It is the amount of reagent in the kit that determines read length. Sometimes index cycle reagents are allocated to R1/R2 or they used anot…
Comment: Why gatk VariantAnnotator required bam and coverage files by Pierre Lindenbaum 161k
you don't need the bam file https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator : VariantAnnotator …
Comment: GAPIT p-value significance threshold by ginellegrenier • 0
Hi, I was wondering if you have found a solution to this? Thanks!
Comment: PCA plot by jkim ▴ 170
cross posted in bioconductor. [https://support.bioconductor.org/p/9157968/][1] [1]: https://support.bioconductor.org/p/9157968/
Comment: ScRNA data question by bk11 ★ 2.3k
Which normalization method did you use for your data? I am guessing you had used SCTransform normalization for your data. Can you plot usin…
Comment: How to make a TSS enrichment plot in ATAC-seq analysis? by sp • 0
Hi Dan, I was wondering if you found out how to make the same graph with NFR and NBR regions with different curves. I was able to recreate…
Comment: Why gatk VariantAnnotator required bam and coverage files by QX • 0
I think the coverage could also computed from bam file itself, but let say I do not include the coverage, do you have any idea why it needs…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas by GenoMax 141k
I am moving my answer to a comment. At this point you should email NCBI help desk and ask them this question. If you get an answer then ple…
Comment: Figures are disappeared from html report of SnpEff by Pierre Lindenbaum 161k
the javascript in your html is deprecated or your firefox is just tool old.
Comment: Why gatk VariantAnnotator required bam and coverage files by Pierre Lindenbaum 161k
> I would like to ask why they may require the bam file for this function? hum.. if you want to add the coverage, where do you think gatk …
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