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412 results • Page 5 of 9
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7
votes
1
reply
2.3k
views
Tutorial: A gentle introduction to biogo
sequence golang biogo
updated 12 months ago by 43k • written 6.6 years ago by ★ 1.7k
7
votes
8
replies
3.4k
views
Tutorial: Determine if a transcription factor is bound with CENTIPEDE
ChIP-Seq transcription-factor DNase-Seq CENTIPEDE
updated 17 months ago by 43k • written 8.9 years ago by ★ 2.3k
7
votes
1
reply
197
views
Tutorial: removeBatchEffect explained using base R linear models
limma effects batch removebatcheffects
updated 11 days ago by 14k • written 11 days ago by ▴ 360
7
votes
2
replies
3.6k
views
Tutorial: List Of Tools For Mapping High-Throughput Sequencing Data (2012)
next-gen mapping
updated 15 months ago by 43k • written 11.6 years ago by 11k
6
votes
0
replies
585
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
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
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
3
replies
5.7k
views
Tutorial: High Throughput Sequence Analysis With R And Bioconductor
bioconductor
updated 15 months ago by 43k • written 11.9 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 15 months ago by 43k • written 11.2 years ago by 11k
6
votes
2
replies
5.1k
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
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
0
replies
5.7k
views
Tutorial: How to download GEO data Quickly and easily
geo RNA-Seq R data-mining
14 months ago by Novogene ▴ 420
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
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
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
1.6k
views
Tutorial: GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma GPL6955 Microarray miRNA Agilent
2.8 years ago by Kevin Blighe 88k
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
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
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
0
replies
3.2k
views
Tutorial: Uc Riverside Bioinformatics Manuals
computing-manuals
updated 15 months ago by 43k • written 12.1 years ago by 26k
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
6
votes
0
replies
6.4k
views
Tutorial: Leveraging Flow Order And Flow Signals From Ion Torrent Data
ion-torrent
updated 15 months ago by 43k • written 12.0 years ago by ▴ 360
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
1
reply
7.8k
views
Tutorial: Expression Analysis Of Rna-Seq Experiments With Tophat And Cufflinks
tophat RNA-seq cufflinks
updated 15 months ago by 43k • written 12.0 years ago by 100k
6
votes
1
reply
486
views
Tutorial: Bulk RNA-seq: Different Expression Analysis
differential-expression RNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
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
0
replies
1.9k
views
Tutorial: Gatk December Workshop Presentations
gatk
updated 15 months ago by 43k • written 11.3 years ago by ★ 5.3k
5
votes
5
replies
673
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 15 days ago by • 0 • written 23 days ago by ★ 3.9k
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
0
replies
1.2k
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
4.2k
views
Tutorial: Chip Seq Review Papers
chip-seq
updated 15 months ago by 43k • written 11.5 years ago by ▴ 80
5
votes
0
replies
1.7k
views
Tutorial: Software Carpentry
programming
updated 15 months ago by 43k • written 12.1 years ago by 8.5k
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 11 months ago by 43k • written 16 months ago by ▴ 420
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
13
replies
2.0k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 28 days ago by 82k • written 29 days ago by ★ 1.7k
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
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
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
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
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
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
0
replies
2.3k
views
Tutorial: Accurate prediction of active enhancers using PARE
ChIP-Seq histone-modification enhancer
updated 12 months ago by 43k • written 7.1 years ago by ▴ 100
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
1
reply
6.1k
views
Tutorial: Chip-Seq Data Analysis Tutorial
chip-seq
updated 15 months ago by 43k • written 12.0 years ago by ▴ 360
4
votes
0
replies
792
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
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
4
votes
0
replies
2.3k
views
Tutorial: Exploring Encode Data In The Ucsc Genome Browser
encode
updated 15 months ago by 43k • written 11.8 years ago by 11k
4
votes
2
replies
2.5k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 14 months ago by 43k • written 4.9 years ago by ★ 9.4k
4
votes
1
reply
3.2k
views
Tutorial: Embo Practical Course On Analysis Of High-Throughput Sequencing Data
sequencing
updated 15 months ago by 43k • written 12.0 years ago by ▴ 360
4
votes
0
replies
1.2k
views
Tutorial: Long Read Genome Assembly Video Series
long-read genome-assembly
3.0 years ago by pbpanigrahi ▴ 420
412 results • Page 5 of 9
Recent Votes
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
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Recent Replies
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors) by nguyenn6 • 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed by anton.i.petrov • 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp by analyst ▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by GenoMax 142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R by 1769mkc ★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks by ATpoint 82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner by Joe 21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression? by Gordon Smyth ★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
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