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411 results • Page 5 of 9
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7
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Tutorial: How to extract fastq files from SRA data that contains both paired and unpaired reads
fastq-dump sra
updated 13 months ago by 43k • written 8.1 years ago by ▴ 850
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
3
replies
2.6k
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
updated 13 months ago by ▴ 110 • written 21 months ago by 87k
6
votes
0
replies
547
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
3
replies
5.7k
views
Tutorial: High Throughput Sequence Analysis With R And Bioconductor
bioconductor
updated 14 months ago by 43k • written 11.8 years ago by 100k
6
votes
0
replies
2.3k
views
Tutorial: data.frames in R: How vectorization can save you time and heartache
R
3.1 years ago by rpolicastro 13k
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 87k
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
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 11.1 years ago by 11k
6
votes
3
replies
4.5k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment sequencing RNA-seq gene
updated 13 months ago by 43k • written 5.5 years ago by ▴ 40
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 9.9 years ago by 8.4k
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
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 11 months ago by 43k • written 6.9 years ago by ★ 1.6k
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 13 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
0
replies
5.5k
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
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
1
reply
452
views
Tutorial: Bulk RNA-seq: Different Expression Analysis
differential-expression RNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
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
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
3.2k
views
Tutorial: Uc Riverside Bioinformatics Manuals
computing-manuals
updated 14 months ago by 43k • written 12.0 years ago by 26k
6
votes
10
replies
5.2k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 13 months ago by 43k • written 6.2 years ago by ▴ 370
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
5
votes
0
replies
2.2k
views
Tutorial: Installing multiprocessor-capable MEME to work with a Slurm job scheduler environment
slurm meme parallel
updated 11 months ago by 43k • written 6.6 years ago by 35k
5
votes
2
replies
2.3k
views
Tutorial: NCBI submissions: SRA and TSA
NCBI TSA SRA RNA-Seq
updated 13 months ago by 43k • written 5.5 years ago by ▴ 50
5
votes
0
replies
1.1k
views
Tutorial: Finding individual motif occurrences with FIMO from the MEME suite
motif meme jaspar fimo
updated 13 months ago by 43k • written 5.4 years ago by 82k
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 13 months ago by 43k • written 5.3 years ago by ▴ 10
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
0
replies
1.7k
views
Tutorial: Software Carpentry
programming
updated 14 months ago by 43k • written 12.0 years ago by 8.4k
5
votes
5
replies
576
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 2 days ago by • 0 • written 10 days ago by ★ 3.9k
5
votes
3
replies
5.4k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 13 months ago by • 0 • written 6.5 years ago by ▴ 130
5
votes
3
replies
4.2k
views
Tutorial: Chip Seq Review Papers
chip-seq
updated 14 months ago by 43k • written 11.4 years ago by ▴ 80
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
13
replies
1.6k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 15 days ago by 82k • written 16 days ago by ★ 1.7k
5
votes
1
reply
4.2k
views
Tutorial: Mini-tutorial: How to fix too-long sequence names in SyMAP
alignment
updated 16 months ago by 43k • written 8.9 years ago by 8.4k
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 14 months ago by 43k • written 11.3 years ago by ★ 5.3k
5
votes
0
replies
3.3k
views
Tutorial: How to run CWL with Nextflow
cwl nextflow
updated 13 months ago by 43k • written 4.2 years ago by ★ 3.5k
5
votes
5
replies
7.0k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq
updated 11 months ago by 43k • written 6.5 years ago by ▴ 130
4
votes
1
reply
3.2k
views
Tutorial: Embo Practical Course On Analysis Of High-Throughput Sequencing Data
sequencing
updated 14 months ago by 43k • written 12.0 years ago by ▴ 360
4
votes
1
reply
1.9k
views
Tutorial: One of the easy way to achieve read count and RPKM file
RNA-Seq
updated 11 months ago by 43k • written 6.7 years ago by ▴ 40
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
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
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
9 months ago by Ming Tommy Tang ★ 3.9k
4
votes
1
reply
6.1k
views
Tutorial: Chip-Seq Data Analysis Tutorial
chip-seq
updated 14 months ago by 43k • written 12.0 years ago by ▴ 360
4
votes
2
replies
2.5k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 13 months ago by 43k • written 4.9 years ago by ★ 9.4k
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
0
replies
783
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 13 months ago by 43k • written 6.1 years ago by ★ 4.0k
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
411 results • Page 5 of 9
Recent Votes
Answer: Should I remove these cells? (scRNA 10x 5')
Answer: STRING-DB API can't find my protein but I can find it when I go to the STRING-DB
Answer: STRING-DB API can't find my protein but I can find it when I go to the STRING-DB
A: Fold change - a final explanation
Answer: sc/snRNASeq using cell ranger parameters
mitochondria in single nuclear RNAseq
Answer: Association study using SNP data
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Answer: DMRcate ranges liftover hg19 to hg38 by aaron.stevens • 0
Hey, I believe they are mapped to hg19 and this is potentially a bigger problem than people realise, I nearly made this mistake and I would…
Comment: STRING-DB API can't find my protein but I can find it when I go to the STRING-DB by brandon • 0
This worked beautifully using 'requests.get()' in python, thank you so much!
Answer: STRING-DB API can't find my protein but I can find it when I go to the STRING-DB by Pierre Lindenbaum 161k
first get the main ID in stringdb: $ wget -qO - "https://string-db.org/api/tsv-no-header/get_string_ids?identifiers=RPS4Y1&species=960…
Comment: Help with DGEList function by marco.barr ▴ 90
Are you sure you've loaded the library properly? Have you checked if edgeR is ticked in the list of installed packages? Double-check it. If…
Comment: Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so t by mropri ▴ 150
Hi, I just wanted to update that IEGscore and PCNAscore were linearly dependent (or linear combinations of each other). I tested this using…
Comment: TaxID mapping file by Lada ▴ 30
if I understood correctly, I might need fle `prot.accession2taxid.gz` file? According to the [documentation][1] in column 2 is Accession.ve…
Answer: install package by Pine ▴ 10
To follow on Mathew's reply, one way might be to try and see if you can download and install the package tarball locally: 1. Get the packag…
Comment: agilent human all exon sureselct v7 bed file by MiladAD ▴ 10
God bless you man.
Answer: install package by Mathew ▴ 50
Hi, This is what happens when I run some code to diagnose the issue. First, I wanted to see what version of R was required for the package…
Comment: TaxID mapping file by Lada ▴ 30
thank you, I'll look at these files/documents. .
Answer: LD-prune variants while maintaining a list of SNPs by Jautis ▴ 540
I was given a solution by a colleague -- it seems a little hacky, but worked really well! > one way to get this to work is to use --clu…
Answer: Association study using SNP data by drajangirija • 0
Hi Matthew, Thank you very much for your inputs. I am working with Neogen genotyping data, which includes GC values less than 0.15.
Comment: Downloading full alignments from Pfam by bef1 • 0
I tried contacting Pfam, they replied that indeed there is an issue on their side with the full alignments, which should be repaired in the…
Comment: Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Expe by Mensur Dlakic ★ 27k
Don't know about others, but I would never contact someone about potential employment based only on their interests and with zero knowledge…
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If you are talking about methylation idat files, they were all migrated from legacy to the data portal. If you are talking about other pl…
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