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323 results • Page 4 of 7
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15
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4
replies
4.2k
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Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 11 weeks ago by 39k • written 2.8 years ago by ▴ 310
50
votes
3
replies
4.2k
views
Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 11 weeks ago by 39k • written 4.4 years ago by 72k
10
votes
3
replies
4.2k
views
Tutorial: Video: Alternative Splicing and Primer Design
RNA-Seq IGB
updated 4 months ago by 39k • written 8.7 years ago by ▴ 860
9
votes
0
replies
4.2k
views
Tutorial: Analysis of dbGaP data on the cloud
AWS dbGaP Cloud
updated 10 months ago by 39k • written 7.3 years ago by 19k
6
votes
3
replies
4.1k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment sequencing RNA-seq gene
updated 11 weeks ago by 39k • written 4.6 years ago by ▴ 40
21
votes
2
replies
4.1k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 8 months ago by ▴ 40 • written 2.1 years ago by 7.9k
4
votes
3
replies
4.0k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy R
updated 11 weeks ago by 39k • written 5.1 years ago by ★ 3.9k
2
votes
0
replies
4.0k
views
Tutorial: Calculation of TSS Scores for ATAC-seq Data
next-gen-sequencing
updated 11 weeks ago by 39k • written 3.9 years ago by ▴ 20
5
votes
1
reply
4.0k
views
Tutorial: Mini-tutorial: How to fix too-long sequence names in SyMAP
alignment
updated 5 months ago by 39k • written 7.9 years ago by 7.8k
3
votes
4
replies
4.0k
views
Tutorial: gencore: a tool to reduce sequencing noises by generating consensus reads
consensus OpenGene sequencing-noise
updated 10 days ago by 39k • written 5.1 years ago by ★ 2.4k
5
votes
3
replies
3.9k
views
Tutorial: Chip Seq Review Papers
chip-seq
updated 3 months ago by 39k • written 10.5 years ago by ▴ 80
9
votes
3
replies
3.9k
views
Tutorial: Ht Sequence Analysis With R And Bioconductor By The Bioinformatics Center At Uc Riverside
bioconductor
updated 3 months ago by 39k • written 10.8 years ago by 98k
28
votes
4
replies
3.8k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 11 weeks ago by 39k • written 4.4 years ago by 26k
9
votes
9
replies
3.7k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
reference-coverage ngs
updated 16 days ago by 39k • written 5.7 years ago by 85k
6
votes
2
replies
3.7k
views
Tutorial: GATK method for filtering vcf lines using GT values at all or multisample level.
genome vcf genotype variant-filtration
updated 20 days ago by 39k • written 6.0 years ago by ★ 1.5k
5
votes
0
replies
3.7k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
updated 11 weeks ago by 39k • written 2.4 years ago by 129k
1
vote
0
replies
3.5k
views
Tutorial: embarrassingly easy parallel in Python, Perl and R
parallel
updated 9 months ago by 39k • written 7.5 years ago by ▴ 70
3
votes
1
reply
3.5k
views
Tutorial: Importance of Array Quality Control - arrayQualityMetrics (PART I)
gene R
updated 8 weeks ago by 39k • written 6.9 years ago by ▴ 140
3
votes
2
replies
3.5k
views
Tutorial: Galaxy Tutorial on ChIP-seq
galaxy ChIP-Seq
updated 21 days ago by 39k • written 6.1 years ago by ▴ 30
6
votes
2
replies
3.5k
views
Tutorial: How to extract fastq files from SRA data that contains both paired and unpaired reads
fastq-dump sra
updated 8 weeks ago by 39k • written 7.2 years ago by ▴ 830
3
votes
0
replies
3.4k
views
Tutorial: Video Tutorial On Conducting Whole-Exome Sequencing Research
exome-sequencing
updated 3 months ago by 39k • written 9.9 years ago by 9.6k
10
votes
2
replies
3.4k
views
Tutorial: Graph visualization with igraph in R
Visualization igraph Graph R Network
updated 21 days ago by 39k • written 6.1 years ago by 26k
6
votes
0
replies
3.4k
views
Tutorial: How to predict genes using a two-pass (iterative) MAKER2 workflow
Assembly
updated 12 weeks ago by 39k • written 9.0 years ago by 7.8k
0
votes
0
replies
3.4k
views
Tutorial: SFA (Stochastic Frontier Analysis) STATA 14
R
updated 14 days ago by 39k • written 5.3 years ago by ▴ 10
0
votes
0
replies
3.4k
views
Tutorial: Park Test for Heteroskedasticity In R Commander
R Park-Test
updated 14 days ago by 39k • written 5.4 years ago by ▴ 10
3
votes
4
replies
3.4k
views
Tutorial: Gene Set Enrichment Analysis on T-BioInfo
gene RNA-Seq
updated 7 days ago by 39k • written 4.6 years ago by ▴ 340
20
votes
14
replies
3.4k
views
Tutorial: Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data visualization and exploration (Windows)
ChIP-Seq visualization Windows EaSeq
updated 8 weeks ago by 39k • written 7.1 years ago by ▴ 460
4
votes
2
replies
3.3k
views
Tutorial: Introduce OpenGene: an open source library for processing NGS data
NGS sequencing Julia OpenGene
updated 11 weeks ago by 39k • written 7.3 years ago by ★ 2.4k
7
votes
2
replies
3.3k
views
Tutorial: List Of Tools For Mapping High-Throughput Sequencing Data (2012)
next-gen mapping
updated 3 months ago by 39k • written 10.6 years ago by 11k
10
votes
2
replies
3.2k
views
Tutorial: How to find PubMed records where you were author (member) as part of a consortium
pubmed
updated 9 months ago by 39k • written 7.5 years ago by 20k
10
votes
0
replies
3.1k
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap
updated 11 weeks ago by 39k • written 2.4 years ago by 129k
19
votes
2
replies
3.1k
views
Tutorial: Beginner's Handbook to Next Generation Sequencing
NGS
updated 21 days ago by 39k • written 6.1 years ago by ▴ 640
7
votes
8
replies
3.0k
views
Tutorial: Determine if a transcription factor is bound with CENTIPEDE
ChIP-Seq transcription-factor DNase-Seq CENTIPEDE
updated 5 months ago by 39k • written 7.9 years ago by ★ 2.2k
4
votes
1
reply
3.0k
views
Tutorial: Embo Practical Course On Analysis Of High-Throughput Sequencing Data
sequencing
updated 3 months ago by 39k • written 11.1 years ago by ▴ 360
14
votes
2
replies
3.0k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 11 weeks ago by 39k • written 2.7 years ago by 2.9k
1
vote
4
replies
3.0k
views
Tutorial: How to install C++ compilers/make from GNU for Gromacs?
Gromacs Cpp-compilers GNU
updated 8 weeks ago by 39k • written 7.0 years ago by ▴ 10
22
votes
1
reply
3.0k
views
Tutorial: Introduction To R Course Materials Available
R
updated 4 months ago by 39k • written 11.1 years ago by 26k
6
votes
0
replies
3.0k
views
Tutorial: Uc Riverside Bioinformatics Manuals
computing-manuals
updated 3 months ago by 39k • written 11.1 years ago by 26k
1
vote
4
replies
3.0k
views
Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq
updated 10 days ago by 39k • written 5.1 years ago by ▴ 340
3
votes
0
replies
3.0k
views
Tutorial: Sorting GFF/GTF files
gtf gff
updated 12 weeks ago by 39k • written 2.9 years ago by 7.9k
1
vote
2
replies
3.0k
views
Tutorial: Standalone BLAST error: UnexpectedTagClassByte
software-error blast
updated 7 months ago by 39k • written 7.8 years ago by ▴ 10
15
votes
1
reply
2.9k
views
Tutorial: Current Topics in Genome Analysis 2016 (collection of educational lectures)
genomics training lectures workshop
updated 8 weeks ago by 39k • written 7.1 years ago by 19k
1
vote
3
replies
2.9k
views
Tutorial: resolving error of sspace_standard
software-error Assembly
updated 7 weeks ago by 39k • written 6.8 years ago by ▴ 300
6
votes
2
replies
2.9k
views
Tutorial: Unsupervised clustering on gene expression data
gene RNA-seq expression clustering
8 months ago by Hamid Ghaedi 2.9k
1
vote
0
replies
2.9k
views
Tutorial: Canadian Bioinformatics Workshops 2016 Series
Assembly SNP RNA-Seq ChIP-Seq alignment
updated 11 months ago by 39k • written 7.4 years ago by ▴ 30
27
votes
0
replies
2.9k
views
Tutorial: Building Docker images
singularity docker container
10 months ago by ATpoint 72k
7
votes
0
replies
2.8k
views
Tutorial: On the concept of constant or intercept used in Differential Expression (DE) analysis
regression limma DESeq2
updated 8 weeks ago by 39k • written 7.1 years ago by ★ 5.1k
5
votes
2
replies
2.8k
views
Tutorial: Get GC Content from UCSC with perl script (mysql)
myql ucsc gc-content perl
updated 21 days ago by 39k • written 6.1 years ago by ★ 9.3k
10
votes
4
replies
2.8k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 13 days ago by 39k • written 5.3 years ago by 85k
0
votes
0
replies
2.8k
views
Tutorial: Normality Test For JB (Jarque Bera) Test R Commander
Jarque-Bera-Test R-Commander
updated 14 days ago by 39k • written 5.5 years ago by ▴ 10
323 results • Page 4 of 7
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Comment: ggsave() bug in ggplot2?
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Answer: Help with running ATAC using Encode pipeline
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Answer: How to extract haplotype data from phased bcf files by Pierre Lindenbaum 154k
use %TGT (translated genotype) $ bcftools query -f '[%CHROM %POS %TGT\n]'
Comment: convert data frame with character column to data frame with integer column by Basti ★ 1.5k
You would better give an example with values because we don't know what is in each variable so we cannot give you a precise code, but seems…
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data. by ATpoint 72k
This information is annotated in GTF files. You can get them for almost every annotated species from Ensembl. There is a column `gene_bioty…
Answer: DE genes across multiple scRNAseq clusters-are they significantly enriched? by ATpoint 72k
First of all, with thousands of DEGs you might want to choose a DE framework that allows testing against a fold change threshold, such as `…
Comment: PacBio Pipeline and Tools for Variant Call by Kiran ▴ 80
Thanks a lot William, I am Clear now
Comment: The famous WGS dataset, Ashkenazi Trio? by cmdcolin ★ 3.0k
what is valuable information to you
Answer: Why weblogo of biopython doesn't work? by minakshiboruahassam • 0
The weblogo3 application is giving same file even if u run the scripts separately on python standalone or whatever. The weblogo command is …
Answer: Make a BedGraph file by rfran010 ▴ 80
I would suggest bedtools makewindows to generate your 3,000bp bins then bedtools coverage to generate fraction of repeats over your windows…
Answer: What is the best way to clean bulk RNA-seq data? by rfran010 ▴ 80
Honestly, I am a fan of visualizing to select a threshold since these can depend on the specific experiment. I would even just run standard…
Answer: Help with running ATAC using Encode pipeline by rfran010 ▴ 80
Read all instructions carefully Specifically, this info is under the "Input JSON file specification" section with details in the followin…
Answer: BioInformatics, Software by rfran010 ▴ 80
There have been some good suggestions, but it seems like you may be asking one of two questions, either (1) how to do bioinformatics? or (2…
Answer: Genome assembly statistical tools by Bryan • 0
I'll follow up what a few others have mentioned, but I like stats.sh within the BBTools package for raw assembly stats. I'll then polish my…
Comment: how to design a guide RNA by rfran010 ▴ 80
I agree this is very basic CRISPR mechanism and you'd be better off reading sites that could explain better than me. However, there is a lo…
Comment: ATAC peak-calling: same peak ID across multiple experimental conditions? by rfran010 ▴ 80
You want to use the MACS2 score columns? You can retain these with bedtools option `-c` . This will retain the score columns from any merge…
Comment: best annotation approach for peaks by rfran010 ▴ 80
The number of regions annotated as "Promoters" is the same regardless of TSS length? You can add this argument to annotatePeak (for mouse M…
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