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232 results • Page 3 of 5
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29
votes
5
replies
5.9k
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Tutorial: Gnu Parallel Tutorial
parallel gnu-parallel
updated 26 days ago by 38k • written 9.5 years ago by ★ 4.3k
4
votes
1
reply
5.8k
views
Tutorial: Chip-Seq Data Analysis Tutorial
chip-seq
updated 4 weeks ago by 38k • written 10.9 years ago by ▴ 360
20
votes
7
replies
5.6k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 12 days ago by 38k • written 4.4 years ago by ▴ 740
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
14
votes
7
replies
5.4k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 12 days ago by 38k • written 6.9 years ago by ★ 3.3k
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
7
votes
0
replies
5.1k
views
Tutorial: Mothur Analyzing 16S Of Ngs High Through-Put Sequencing
next-gen
updated 4 weeks ago by 38k • written 10.8 years ago by ▴ 120
34
votes
15
replies
5.0k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 12 days ago by 38k • written 3.8 years ago by ★ 9.3k
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
20
votes
6
replies
4.8k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 12 days ago by 38k • written 6.5 years ago by ★ 5.2k
12
votes
1
reply
4.8k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 12 days ago by 38k • written 3.0 years ago by 4.6k
12
votes
31
replies
4.7k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 17 days ago by 38k • written 3.6 years ago by 7.7k
12
votes
1
reply
4.7k
views
Tutorial: RepSeq data processing and analysis
immunology tcr repseq sequencing repertoire
updated 5 months ago by 38k • written 7.6 years ago by 3.5k
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
20
votes
10
replies
4.6k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 12 days ago by 38k • written 2.6 years ago by 11k
3
votes
0
replies
4.5k
views
Tutorial: Comparing 454, Iontorrent And Miseq
454 miseq ion-torrent
updated 4 weeks ago by 38k • written 10.9 years ago by 97k
11
votes
6
replies
4.5k
views
Tutorial: sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 8 months ago by 38k • written 7.1 years ago by ★ 4.1k
6
votes
11
replies
4.5k
views
6 follow
Tutorial: Add count numbers to headers in a fasta file
genome
updated 6 weeks ago by 38k • written 6.3 years ago by ▴ 50
7
votes
0
replies
4.5k
views
Tutorial: How To Perform A Hierarchical Clustering Using Interactive Heatmaps From Gitools?
clustering
updated 23 days ago by 38k • written 9.0 years ago by ▴ 990
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
10
votes
0
replies
4.5k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 12 days ago by 38k • written 2.2 years ago by 127k
10
votes
7
replies
4.5k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 12 days ago by 38k • written 2.5 years ago by 84k
12
votes
4
replies
4.4k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 6 weeks ago by 38k • written 2.1 years ago by ▴ 120
6
votes
10
replies
4.3k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 12 days ago by 38k • written 5.1 years ago by ▴ 340
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
9
votes
0
replies
4.1k
views
Tutorial: Analysis of dbGaP data on the cloud
AWS dbGaP Cloud
updated 8 months ago by 38k • written 7.1 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 days ago by 38k • written 4.4 years ago by ▴ 40
15
votes
4
replies
4.1k
views
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
13
votes
9
replies
4.0k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 9 months ago by ▴ 40 • written 15 months ago by ★ 1.1k
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
5
votes
1
reply
3.9k
views
Tutorial: Mini-tutorial: How to fix too-long sequence names in SyMAP
alignment
updated 3 months ago by 38k • written 7.8 years ago by 7.7k
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
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
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
2
votes
0
replies
3.8k
views
Tutorial: Calculation of TSS Scores for ATAC-seq Data
next-gen-sequencing
updated 12 days ago by 38k • written 3.7 years ago by ▴ 20
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
28
votes
4
replies
3.7k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 11 days ago by 38k • written 4.2 years ago by 26k
1
vote
0
replies
3.5k
views
Tutorial: embarrassingly easy parallel in Python, Perl and R
parallel
updated 7 months ago by 38k • written 7.4 years ago by ▴ 70
5
votes
0
replies
3.5k
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 12 days ago by 38k • written 2.2 years ago by 127k
3
votes
0
replies
3.4k
views
Tutorial: Video Tutorial On Conducting Whole-Exome Sequencing Research
exome-sequencing
updated 27 days ago by 38k • written 9.8 years ago by 9.5k
6
votes
0
replies
3.4k
views
Tutorial: How to predict genes using a two-pass (iterative) MAKER2 workflow
Assembly
updated 20 days ago by 38k • written 8.8 years ago by 7.7k
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
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
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
13
votes
8
replies
3.1k
views
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
aspera ascp
4 months ago by ATpoint 70k
4
votes
1
reply
3.0k
views
Tutorial: Embo Practical Course On Analysis Of High-Throughput Sequencing Data
sequencing
updated 4 weeks ago by 38k • written 10.9 years ago by ▴ 360
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 3 months ago by 38k • written 7.7 years ago by ★ 2.1k
22
votes
1
reply
3.0k
views
Tutorial: Introduction To R Course Materials Available
R
updated 11 weeks ago by 38k • written 10.9 years ago by 26k
6
votes
0
replies
3.0k
views
Tutorial: Uc Riverside Bioinformatics Manuals
computing-manuals
updated 4 weeks ago by 38k • written 10.9 years ago by 26k
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
232 results • Page 3 of 5
Recent Votes
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
Answer: Hard clip fastq
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Popular Question to sharmatina189059 ▴ 110
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Recent Replies
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…
Answer: Adding median value to VlnPlot in Seurat by Ming Tommy Tang ★ 2.9k
If you know ggplot2, you can `get_expression_data` function in here https://divingintogeneticsandgenomics.rbind.io/post/how-to-do-gene-corr…
Answer: how to know what adapter sequences to trim for RNA-seq? by Ming Tommy Tang ★ 2.9k
You may use fastp which detect adaptors by itself https://github.com/OpenGene/fastp#adapters
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