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412 results • Page 5 of 9
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7
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2
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3.6k
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Tutorial: List Of Tools For Mapping High-Throughput Sequencing Data (2012)
next-gen mapping
updated 14 months ago by 43k • written 11.6 years ago by 11k
7
votes
0
replies
3.0k
views
Tutorial: On the concept of constant or intercept used in Differential Expression (DE) analysis
regression limma DESeq2
updated 13 months ago by 43k • written 8.0 years ago by ★ 5.1k
7
votes
0
replies
4.7k
views
Tutorial: How To Perform A Hierarchical Clustering Using Interactive Heatmaps From Gitools?
clustering
updated 14 months ago by 43k • written 10.2 years ago by ▴ 990
7
votes
0
replies
606
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
9 months ago by barslmn ★ 2.1k
6
votes
2
replies
1.6k
views
Tutorial: GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma GPL6955 Microarray miRNA Agilent
2.7 years ago by Kevin Blighe 88k
6
votes
0
replies
1.6k
views
Tutorial: NCBI dbVar releases updated human reference structural variation (SV) data files and tutorials
dbvar structural-variation
updated 14 months ago by 43k • written 5.5 years ago by ▴ 70
6
votes
1
reply
3.0k
views
Tutorial: Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
ChIP-Seq peak-calling sequencing
updated 14 months ago by 43k • written 10.1 years ago by ▴ 220
6
votes
3
replies
5.7k
views
Tutorial: High Throughput Sequence Analysis With R And Bioconductor
bioconductor
updated 14 months ago by 43k • written 11.9 years ago by 100k
6
votes
3
replies
4.5k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment sequencing RNA-seq gene
updated 14 months ago by 43k • written 5.6 years ago by ▴ 40
6
votes
0
replies
5.6k
views
Tutorial: How to download GEO data Quickly and easily
geo RNA-Seq R data-mining
14 months ago by Novogene ▴ 420
6
votes
1
reply
472
views
Tutorial: Bulk RNA-seq: Different Expression Analysis
differential-expression RNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
6
votes
0
replies
3.2k
views
Tutorial: Uc Riverside Bioinformatics Manuals
computing-manuals
updated 14 months ago by 43k • written 12.1 years ago by 26k
6
votes
2
replies
2.7k
views
Tutorial: Tutorial Bioinformatics Static Website
website
updated 14 months ago by 43k • written 10.3 years ago by ▴ 610
6
votes
1
reply
2.6k
views
Tutorial: Nice simple interactive Vim tutorial
vim linux
updated 14 months ago by 43k • written 9.5 years ago by 9.7k
6
votes
0
replies
571
views
Tutorial: 12 useful command line tools and tricks for genomics data science
unix
updated 3 months ago by 11k • written 3 months ago by ★ 3.9k
6
votes
0
replies
3.6k
views
Tutorial: How to predict genes using a two-pass (iterative) MAKER2 workflow
Assembly
updated 14 months ago by 43k • written 10.0 years ago by 8.5k
6
votes
11
replies
5.7k
views
6 follow
Tutorial: Add count numbers to headers in a fasta file
genome
updated 15 months ago by 43k • written 7.4 years ago by ▴ 50
6
votes
0
replies
6.4k
views
Tutorial: Leveraging Flow Order And Flow Signals From Ion Torrent Data
ion-torrent
updated 14 months ago by 43k • written 12.0 years ago by ▴ 360
6
votes
5
replies
7.0k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq
updated 12 months ago by 43k • written 6.5 years ago by ▴ 140
6
votes
10
replies
5.3k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 14 months ago by 43k • written 6.2 years ago by ▴ 380
6
votes
2
replies
5.0k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
5 months ago by GenoMax 142k
6
votes
1
reply
7.8k
views
Tutorial: Expression Analysis Of Rna-Seq Experiments With Tophat And Cufflinks
tophat RNA-seq cufflinks
updated 14 months ago by 43k • written 12.0 years ago by 100k
6
votes
4
replies
7.5k
views
Tutorial: Overlay Multiple Tracks In Ucsc Browser [Quick Minimal Tutorial]
visualization ChIP-seq RNA-seq ucsc-genome-browser bigwig
updated 14 months ago by 43k • written 11.2 years ago by 11k
6
votes
2
replies
4.2k
views
Tutorial: GATK method for filtering vcf lines using GT values at all or multisample level.
genome vcf genotype variant-filtration
updated 12 months ago by 43k • written 7.0 years ago by ★ 1.6k
6
votes
0
replies
2.4k
views
Tutorial: data.frames in R: How vectorization can save you time and heartache
R
3.1 years ago by rpolicastro 13k
5
votes
2
replies
2.3k
views
Tutorial: NCBI submissions: SRA and TSA
NCBI TSA SRA RNA-Seq
updated 14 months ago by 43k • written 5.5 years ago by ▴ 50
5
votes
0
replies
2.2k
views
Tutorial: Installing multiprocessor-capable MEME to work with a Slurm job scheduler environment
slurm meme parallel
updated 12 months ago by 43k • written 6.7 years ago by 35k
5
votes
5
replies
648
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 10 days ago by • 0 • written 19 days ago by ★ 3.9k
5
votes
2
replies
1.7k
views
Tutorial: ENCODE 2016: Research Applications and Users Meeting
ChIP-Seq next-gen ENCODE
updated 13 months ago by 43k • written 7.9 years ago by ★ 1.1k
5
votes
2
replies
2.3k
views
Tutorial: Using Bedtools Closest (closestBed) to make distance histograms of protein binding frequency near all types of pre-RNA junctions (e.g. exon-intron an…
preRNA closestBed bedtools-closest bedtools
updated 14 months ago by 43k • written 5.3 years ago by ▴ 10
5
votes
13
replies
1.8k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 23 days ago by 82k • written 24 days ago by ★ 1.7k
5
votes
0
replies
3.3k
views
Tutorial: How to run CWL with Nextflow
cwl nextflow
updated 14 months ago by 43k • written 4.2 years ago by ★ 3.5k
5
votes
0
replies
1.7k
views
Tutorial: Software Carpentry
programming
updated 14 months ago by 43k • written 12.1 years ago by 8.5k
5
votes
0
replies
1.9k
views
Tutorial: Gatk December Workshop Presentations
gatk
updated 14 months ago by 43k • written 11.3 years ago by ★ 5.3k
5
votes
0
replies
1.7k
views
Tutorial: GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo RNA-Seq data-mining SRA
updated 10 months ago by 43k • written 16 months ago by ▴ 420
5
votes
0
replies
1.1k
views
Tutorial: Finding individual motif occurrences with FIMO from the MEME suite
motif meme jaspar fimo
updated 14 months ago by 43k • written 5.5 years ago by 82k
5
votes
3
replies
5.4k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 14 months ago by • 0 • written 6.6 years ago by ▴ 140
5
votes
1
reply
4.2k
views
Tutorial: Mini-tutorial: How to fix too-long sequence names in SyMAP
alignment
updated 17 months ago by 43k • written 8.9 years ago by 8.5k
5
votes
2
replies
3.1k
views
Tutorial: Get GC Content from UCSC with perl script (mysql)
myql ucsc gc-content perl
updated 12 months ago by 43k • written 7.1 years ago by ★ 9.4k
5
votes
3
replies
4.2k
views
Tutorial: Chip Seq Review Papers
chip-seq
updated 14 months ago by 43k • written 11.5 years ago by ▴ 80
4
votes
2
replies
2.9k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 8 months ago by 142k • written 4.0 years ago by 82k
4
votes
0
replies
964
views
Tutorial: How to make a heatmap in R and deep understand it
heatmap r
12 months ago by Ming Tommy Tang ★ 3.9k
4
votes
0
replies
787
views
Tutorial: How to do GSEA in R for RNAseq data
gsea RNAseq rstats
10 months ago by Ming Tommy Tang ★ 3.9k
4
votes
0
replies
1.2k
views
Tutorial: Long Read Genome Assembly Video Series
long-read genome-assembly
2.9 years ago by pbpanigrahi ▴ 420
4
votes
2
replies
7.2k
views
Tutorial: Analyzing Genomewide Association Study Data: A Tutorial Using Plink
plink gwas
updated 14 months ago by 43k • written 12.0 years ago by 100k
4
votes
2
replies
1.1k
views
Tutorial: How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC transcription factor ChIP-seq
10 months ago by Ming Tommy Tang ★ 3.9k
4
votes
1
reply
1.4k
views
Tutorial: Real World BEDtools. Practical Examples for Variant Filtering and Gene Annotations
BED BEDtools
updated 14 months ago by 43k • written 3.8 years ago by ▴ 40
4
votes
2
replies
3.6k
views
Tutorial: Introduce OpenGene: an open source library for processing NGS data
NGS sequencing Julia OpenGene
updated 14 months ago by 43k • written 8.2 years ago by ★ 2.5k
4
votes
0
replies
1.8k
views
Tutorial: NIH CDE browser for TCGA clinical data CDE codes
nih tcga metadata cde
updated 14 months ago by 43k • written 4.1 years ago by 88k
4
votes
3
replies
4.6k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy R
updated 14 months ago by 43k • written 6.1 years ago by ★ 4.0k
412 results • Page 5 of 9
Recent Votes
Answer: Is there any way to modify this pie chart ?
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
A: How can I convert -log10 (p-value) to p-value?
Comment: What does the 'E%' represent in BUSCO results?
Answer: What does the 'E%' represent in BUSCO results?
Answer: Combine Two Affymetrix Datasets With Same Platform
Comment: Kraken2 database
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Recent Replies
Comment: Is it necessary to do genotype quality filteration after snp calling with GATK by IdaHao0921 • 0
The species I study is not a model species, VQSR can not be applied here. I already used gatk hard-filtering. I mean, after hard-filtering,…
Answer: Overlapping Ranges within Granges object by Alex Reynolds 35k
If you're not tied to Granges, you could use `bedmap --fraction-both 0.1` to require at least 10% overlap between reference and map regions…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred by Vijith ▴ 30
By doing some online search, I tried installing one module `cpan Bio::DB::Fasta` and it is running like a never-ending installation process…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred by Vijith ▴ 30
I have tried installing AGAT. But it failed the tests. …
Comment: BWA alignment by ATpoint 82k
That is not what the logs above tell, but good you solved it.
Answer: Inquiry about deseq2 transformation by ATpoint 82k
The transformations first correct for sequencing depth (and [composition][1]) and then apply the variance stabilization / regularization. N…
Answer: The total expressed genes in RNA-Seq data by ATpoint 82k
There is no robust definition of "expressed" genes, this has been asked many times before. edgeR doesn't care about "expressed", it cares (…
Answer: What is the bin size for Bamcompare? by ATpoint 82k
It is the number of adjacent bases that are aggregated (binned) into a single value. I find binning not optimal, and would always set this …
Comment: Is it necessary to do genotype quality filteration after snp calling with GATK by Pierre Lindenbaum 161k
see VQSR https://gatk.broadinstitute.org/hc/en-us/articles/360035531612-Variant-Quality-Score-Recalibration-VQSR and https://gatk.broadinst…
Comment: Snakemake wrapper issue by Matvii Mykhailichenko • 0
Hi, I kind of did and kind of didn't: I stopped trying to use snakemake( I remember that it's a lot of hustle to install pickard, maybe you…
Answer: Is there any way to modify this pie chart ? by marco.barr ▴ 110
Hi, you can add the labels outside chart using `geom_label_repel` from `ggrepel` package. Check out this guide [https://r-charts.com/part…
Answer: Snakemake wrapper issue by Wei-Chen Pan • 0
Hi, did you solve your problem ? I also encounter same issue but it's `wrapper:"v3.9.0/bio/picard/mergevcfs"`. In my log file, it said:…
Comment: What does the 'E%' represent in BUSCO results? by Philipp Bayer 8.5k
No worries! I found the commit with the maths too: https://gitlab.com/ezlab/busco/-/blame/master/src/busco/busco_tools/hmmer.py?page=2#L135…
Comment: What does the 'E%' represent in BUSCO results? by 林明德 • 0
Thank you for your answer! It really helped me resolve a doubt!
Answer: What does the 'E%' represent in BUSCO results? by Philipp Bayer 8.5k
Ah your edit solved this. 50 BUSCOs contain internal stop codons, indicating they might be erroneous gene models, or the genes themselves a…
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