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232 results • Page 3 of 5
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15
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4
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Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 12 days ago by 38k • written 2.7 years ago by ▴ 300
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
34
votes
4
replies
5.5k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 4 months ago by 38k • written 7.7 years ago by ▴ 370
12
votes
4
replies
1.8k
views
Tutorial: Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR DESeq2
updated 3 days ago by 38k • written 5.5 years ago by ▴ 570
20
votes
4
replies
2.2k
views
Tutorial: Bash One-liners collection on Github
bash linux shell
updated 12 days ago by 38k • written 3.9 years ago by ▴ 180
13
votes
3
replies
4.7k
views
Tutorial: Video: Visualization of whole genome DNA methylation data in IGB
Bismark BS-Seq RNA-Seq IGB
updated 10 months ago by 38k • written 8.0 years ago by ▴ 860
1
vote
3
replies
417
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbs sampling splice
updated 3 months ago by 127k • written 3 months ago by ★ 1.3k
6
votes
3
replies
4.1k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment sequencing RNA-seq gene
updated 11 days ago by 38k • written 4.4 years ago by ▴ 40
50
votes
3
replies
4.0k
views
Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 12 days ago by 38k • written 4.2 years ago by 70k
9
votes
3
replies
3.9k
views
Tutorial: Ht Sequence Analysis With R And Bioconductor By The Bioinformatics Center At Uc Riverside
bioconductor
updated 4 weeks ago by 38k • written 10.6 years ago by 97k
8
votes
3
replies
2.5k
views
Tutorial: Free online interactive Ensembl training
ensembl training genome
updated 8 months ago by 38k • written 7.1 years ago by 23k
10
votes
3
replies
4.1k
views
Tutorial: Video: Alternative Splicing and Primer Design
RNA-Seq IGB
updated 9 weeks ago by 38k • written 8.5 years ago by ▴ 860
5
votes
3
replies
3.9k
views
Tutorial: Chip Seq Review Papers
chip-seq
updated 4 weeks ago by 38k • written 10.3 years ago by ▴ 80
4
votes
3
replies
3.9k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy R
updated 12 days ago by 38k • written 5.0 years ago by ★ 3.9k
6
votes
3
replies
5.4k
views
Tutorial: High Throughput Sequence Analysis With R And Bioconductor
bioconductor
updated 4 weeks ago by 38k • written 10.7 years ago by 97k
51
votes
3
replies
22k
views
Tutorial: Sam File Format - Lesser Known Tips And Tricks
sam
updated 4 weeks ago by 38k • written 10.2 years ago by ▴ 300
1
vote
3
replies
1.4k
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC TCGABiolinks STAR
updated 5 weeks ago by 38k • written 11 months ago by ★ 1.7k
0
votes
3
replies
2.3k
views
Tutorial: Automatic Primer Design
Assembly sequence
updated 7 months ago by 38k • written 7.4 years ago by ▴ 40
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
5
votes
3
replies
4.5k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 10 days ago by • 0 • written 5.4 years ago by ▴ 130
12
votes
2
replies
1.0k
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R
updated 12 days ago by 38k • written 2.0 years ago by 11k
6
votes
2
replies
2.4k
views
Tutorial: Unsupervised clustering on gene expression data
gene RNA-seq expression clustering
6 months ago by Hamid Ghaedi 2.9k
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
6
votes
2
replies
2.4k
views
Tutorial: Tutorial Bioinformatics Static Website
website
updated 24 days ago by 38k • written 9.2 years ago by ▴ 610
3
votes
2
replies
4.9k
views
Tutorial: Reorder Vcf Files
vcf
updated 4 weeks ago by 38k • written 9.9 years ago by ▴ 60
7
votes
2
replies
3.3k
views
Tutorial: List Of Tools For Mapping High-Throughput Sequencing Data (2012)
next-gen mapping
updated 4 weeks ago by 38k • written 10.5 years ago by 11k
15
votes
2
replies
2.7k
views
Tutorial: Introduction to bedtools.
bedtools
updated 17 days ago by 38k • written 8.4 years ago by 11k
2
votes
2
replies
1.5k
views
Tutorial: Human mitochondrial DNA annotation in SnpEff
chrMT SNP snpEff
updated 12 days ago by 38k • written 2.7 years ago by 3.1k
5
votes
2
replies
807
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
5 weeks ago by Kevin Blighe 84k
3
votes
2
replies
2.0k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
blogs Workshops conferences tutorials
updated 28 days ago by ▴ 970 • written 5.9 years ago by ▴ 100
4
votes
2
replies
2.0k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 12 days ago by 38k • written 3.8 years ago by ★ 9.3k
45
votes
2
replies
35k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 5 weeks ago by 38k • written 11.0 years ago by ▴ 540
5
votes
2
replies
2.0k
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 12 days ago by 38k • written 4.2 years ago by ▴ 10
60
votes
2
replies
6.9k
views
Tutorial: Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 4 weeks ago by 38k • written 10.6 years ago by 97k
1
vote
2
replies
546
views
Tutorial: ViennaRNA package installation in Windows
install mfold viennarna rna windows
updated 6 months ago by 9.6k • written 6 months ago by ▴ 20
42
votes
2
replies
17k
views
Tutorial: Sequencing Technology Review Papers
sequencing papers
updated 4 weeks ago by 38k • written 10.6 years ago by 97k
0
votes
2
replies
2.4k
views
Tutorial: Webinar on 'An integrated RNA and DNA approach to unravel genetic regulation in cancer' on 25 Feb
SNP cancer gene-regulation multiomics rna-seq
updated 11 months ago by 38k • written 8.1 years ago by ▴ 70
79
votes
2
replies
53k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 27 days ago by 38k • written 9.7 years ago by 11k
15
votes
2
replies
6.5k
views
Tutorial: Genotype And Snp Calling Review Papers
snp
updated 4 weeks ago by 38k • written 10.6 years ago by 97k
1
vote
2
replies
2.9k
views
Tutorial: Standalone BLAST error: UnexpectedTagClassByte
software-error blast
updated 5 months ago by 38k • written 7.6 years ago by ▴ 10
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
15
votes
2
replies
1.4k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 5 months ago by ▴ 810 • written 18 months ago by ▴ 270
21
votes
2
replies
3.7k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 6 months ago by ▴ 40 • written 23 months ago by 7.7k
4
votes
2
replies
6.8k
views
Tutorial: Analyzing Genomewide Association Study Data: A Tutorial Using Plink
plink gwas
updated 4 weeks ago by 38k • written 10.8 years ago by 97k
4
votes
2
replies
3.3k
views
Tutorial: Introduce OpenGene: an open source library for processing NGS data
NGS sequencing Julia OpenGene
updated 11 days ago by 38k • written 7.1 years ago by ★ 2.4k
10
votes
2
replies
3.1k
views
Tutorial: How to find PubMed records where you were author (member) as part of a consortium
pubmed
updated 7 months ago by 38k • written 7.4 years ago by 20k
5
votes
2
replies
2.0k
views
Tutorial: NCBI submissions: SRA and TSA
NCBI TSA SRA RNA-Seq
updated 9 days ago by 38k • written 4.3 years ago by ▴ 50
14
votes
2
replies
2.8k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 12 days ago by 38k • written 2.5 years ago by 2.9k
6
votes
1
reply
7.6k
views
Tutorial: Expression Analysis Of Rna-Seq Experiments With Tophat And Cufflinks
tophat RNA-seq cufflinks
updated 4 weeks ago by 38k • written 10.9 years ago by 97k
1
vote
1
reply
471
views
Tutorial: Converting TSV file to VCF
vcf preprocessing frequency
updated 10 weeks ago by 153k • written 10 weeks ago by ★ 1.3k
232 results • Page 3 of 5
Recent Votes
A: circos plot gene expression by RNA-Seq
Create Interval List for Picard CollectRNASeqmetrics
Answer: multiallelic variants
Answer: LIMMA calculates identical adj.P.Val for different proteins from proteomics
Comment: Hard clip fastq
Answer: Hard clip fastq
Answer: Hard clip fastq
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Recent Replies
Answer: getTable ignores query ranges by Kyle • 0
The short answer is you can theoretically do this you just need to a) make your SNPs are two base-pairs in length (i.e. add 1 to the end) a…
Answer: Installing rlang version 1.1.0 by Lluís R. ★ 1.2k
Having a package duplicated means they are at a different `.libPaths()` sites. Check which version is in which directory and directly remov…
Answer: Somatic truth set by samuel ▴ 180
I think I have found an naswer to my own question. Should anyone have the same question as of March 2023 the relevant data and information…
Answer: GetBM - GERP conservation score for GRCm39 by Kyle • 0
Final solution thanks to Ben's help:: # convert df to Grange. snp_gr <-makeGRangesFromDataFrame(BM_SNPs, seqnames.field = "seqnam…
Comment: GetBM - GERP conservation score for GRCm39 by Kyle • 0
Perfect answer, thanks Ben!
Answer: MapSplice2 gives error if the thread count (-p value) is greater than 2 by vishal.koparde ▴ 10
Any updates??
Comment: how to know what adapter sequences to trim for RNA-seq? by lunarskye222 • 0
Do you happen to know if the middle part of this udi barcode (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCTACATATCTCG) is also part of the TruSeq a…
Comment: Hard clip fastq by GenoMax 127k
If you simply want the reads to be compatible in length then do not adapter trim.
Comment: Hard clip fastq by samuel ▴ 180
@ATpoint, so no adapter trimming first? Just trim the raw fastq?
Answer: Confused on strandedness, what are antisense transcripts? by dsull ★ 4.0k
Think of it on the DNA level: If the mRNA made is the same sequence as the "sense" DNA strand (except U's instead of T's), it is a "sense" …
Comment: Protein name in GenBank by GenoMax 127k
If you must do this programmatically then collect all cases where things differ in order of words (or number of words) like the example abo…
Answer: Hard clip fastq by GenoMax 127k
You can also use `reformat.sh` from [**BBMap suite**][1] as follows reformat.sh -Xmx2g in1=R1.fq.gz in2=R2.fq.gz out1=R1_trim.fq.gz …
Answer: Hard clip fastq by ATpoint 70k
Use `seqtk trimfq`. It makes sense to trim first to your desired length and then run identical downstream processing for a fair comparison.…
Comment: Protein name in GenBank by Mensur Dlakic ★ 23k
I think you either take time to do it properly, or you will end up missing some proteins. BLAST sequence search, even on 1500 genomes, can …
Comment: Log2 FC Threshold by ATpoint 70k
Since OP is using GEO2R which uses limma the appropriate function (need to run manually, GEO2R does not support) is `limma::treat()` rather…
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