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411 results • Page
4 of 9
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Views
Votes
Replies
23
votes
2
replies
5.8k
views
Tutorial:
Extracting genomic feature sequences from GTF/GFF files with AGAT
extract
GTF
GFF
sequence
updated 20 months ago by
eggrandio
▴ 40 • written 3.0 years ago by
Juke34
8.6k
6
votes
3
replies
5.7k
views
Tutorial:
High Throughput Sequence Analysis With R And Bioconductor
bioconductor
updated 14 months ago by
Ram
43k • written 11.8 years ago by
Istvan Albert
100k
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
Ram
43k • written 7.4 years ago by
wu.zhiqiang.1020
▴ 50
20
votes
6
replies
5.6k
views
Tutorial:
Open Targets and programmatic access
open-targets
disease
API
drug
updated 13 months ago by
Ram
43k • written 7.6 years ago by
Denise CS
★ 5.2k
10
votes
4
replies
5.6k
views
Tutorial:
Unsupervised clustering on gene expression data
gene-expression
clustering
RNA-seq
8 months ago by
Hamid Ghaedi
3.2k
9
votes
2
replies
5.5k
views
Tutorial:
From Data import to Normalization in Microarray Analysis using in R (Part I)
gene
R
updated 13 months ago by
Ram
43k • written 7.9 years ago by
majuang66
▴ 140
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
23
votes
8
replies
5.4k
views
Tutorial:
A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data
450K
methylation
updated 2.4 years ago by
Ram
43k • written 9.7 years ago by
brentp
24k
12
votes
4
replies
5.4k
views
Tutorial:
*FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux
R
updated 15 months ago by
Ram
43k • written 3.2 years ago by
garden_giessen
▴ 130
0
votes
2
replies
5.4k
views
Tutorial:
Install AMOS on Ubuntu 13.10
sequencing
alignment
software-error
next-gen
updated 2.5 years ago by
Ram
43k • written 9.8 years ago by
Medhat
9.7k
5
votes
3
replies
5.4k
views
Tutorial:
bam2rpkm by bedtools
bam
RNA-Seq
bedtools
rpkm
updated 13 months ago by
toxin08x
• 0 • written 6.5 years ago by
jmzeng1314
▴ 130
7
votes
0
replies
5.3k
views
Tutorial:
Mothur Analyzing 16S Of Ngs High Through-Put Sequencing
next-gen
updated 14 months ago by
Ram
43k • written 11.9 years ago by
Shuixia100
▴ 120
3
votes
2
replies
5.3k
views
Tutorial:
Reorder Vcf Files
vcf
updated 14 months ago by
Ram
43k • written 11.0 years ago by
chris.mit7
▴ 60
6
votes
10
replies
5.2k
views
Tutorial:
Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR
dna-methylation
updated 13 months ago by
Ram
43k • written 6.2 years ago by
dec986
▴ 370
13
votes
3
replies
5.1k
views
Tutorial:
Video: Visualization of whole genome DNA methylation data in IGB
Bismark
BS-Seq
RNA-Seq
IGB
updated 23 months ago by
Ram
43k • written 9.1 years ago by
Nowlan Freese
▴ 860
12
votes
1
reply
5.1k
views
Tutorial:
RepSeq data processing and analysis
immunology
tcr
repseq
sequencing
repertoire
updated 18 months ago by
Ram
43k • written 8.7 years ago by
mikhail.shugay
3.5k
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
12
votes
6
replies
5.0k
views
Tutorial:
sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 21 months ago by
Ram
43k • written 8.2 years ago by
zizigolu
★ 4.3k
10
votes
0
replies
4.9k
views
Tutorial:
Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap
updated 13 months ago by
Ram
43k • written 3.3 years ago by
GenoMax
142k
50
votes
3
replies
4.8k
views
Tutorial:
[[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 13 months ago by
Ram
43k • written 5.3 years ago by
ATpoint
82k
3
votes
0
replies
4.8k
views
Tutorial:
Comparing 454, Iontorrent And Miseq
454
miseq
ion-torrent
updated 14 months ago by
Ram
43k • written 12.0 years ago by
Istvan Albert
100k
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
Ram
43k • written 10.2 years ago by
Michi
▴ 990
2
votes
0
replies
4.7k
views
Tutorial:
Calculation of TSS Scores for ATAC-seq Data
next-gen-sequencing
updated 13 months ago by
Ram
43k • written 4.8 years ago by
Sael
▴ 20
16
votes
3
replies
4.7k
views
Tutorial:
NCBI blast tutorial
ncbi
blast
updated 13 months ago by
Ram
43k • written 8.0 years ago by
Eric Normandeau
11k
15
votes
4
replies
4.6k
views
Tutorial:
RNASeq tutorial for gene differential expression analysis
Transcriptomics
bioconductor
RNA-Seq
R
updated 13 months ago by
Ram
43k • written 3.8 years ago by
Thind amarinder
▴ 340
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
Ram
43k • written 6.1 years ago by
Daniel
★ 4.0k
1
vote
0
replies
4.6k
views
Tutorial:
Molecular docking, estimating free energies of binding, and a tutorial for how to use AutoDock's semi-empirical force field
free-energy
docking
scoring
updated 2.4 years ago by
Ram
43k • written 9.8 years ago by
se.raschka
▴ 150
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
Ram
43k • written 5.5 years ago by
contact
▴ 40
29
votes
4
replies
4.5k
views
Tutorial:
Modern Statistics for Modern Biology
statistics
updated 13 months ago by
Ram
43k • written 5.3 years ago by
Jean-Karim Heriche
27k
10
votes
3
replies
4.5k
views
Tutorial:
Video: Alternative Splicing and Primer Design
RNA-Seq
IGB
updated 15 months ago by
Ram
43k • written 9.6 years ago by
Nowlan Freese
▴ 860
3
votes
4
replies
4.5k
views
Tutorial:
gencore: a tool to reduce sequencing noises by generating consensus reads
consensus
OpenGene
sequencing-noise
updated 11 months ago by
Ram
43k • written 6.0 years ago by
chen
★ 2.5k
9
votes
0
replies
4.4k
views
Tutorial:
Analysis of dbGaP data on the cloud
AWS
dbGaP
Cloud
updated 21 months ago by
Ram
43k • written 8.3 years ago by
Malachi Griffith
19k
16
votes
3
replies
4.4k
views
Tutorial:
Methylation Analysis Tutorial in R_part2
cancer
methylation
RNA-Seq
R
updated 3.2 years ago by
zhuanggj706
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
9
votes
3
replies
4.2k
views
Tutorial:
Ht Sequence Analysis With R And Bioconductor By The Bioinformatics Center At Uc Riverside
bioconductor
updated 14 months ago by
Ram
43k • written 11.7 years ago by
Istvan Albert
100k
9
votes
9
replies
4.2k
views
Tutorial:
Determine % of reference genome covered by aligned SAM/BAM
reference-coverage
ngs
updated 11 months ago by
Ram
43k • written 6.6 years ago by
Kevin Blighe
87k
5
votes
3
replies
4.2k
views
Tutorial:
Chip Seq Review Papers
chip-seq
updated 14 months ago by
Ram
43k • written 11.4 years ago by
prtimilsina
▴ 80
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
Ram
43k • written 6.9 years ago by
kirannbishwa01
★ 1.6k
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
Ram
43k • written 8.9 years ago by
Philipp Bayer
8.4k
10
votes
6
replies
4.2k
views
Tutorial:
CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation
corlevelplot
updated 5 weeks ago by
Ram
43k • written 6.2 years ago by
Kevin Blighe
87k
20
votes
14
replies
4.0k
views
Tutorial:
Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data visualization and exploration (Windows)
ChIP-Seq
visualization
Windows
EaSeq
updated 13 months ago by
Ram
43k • written 8.0 years ago by
Mads Lerdrup
▴ 460
15
votes
1
reply
4.0k
views
Tutorial:
Dealing with nanopore fast5 files compressed with vbz
hdf5
nanopore
fast5
vbz
MinKNOW
updated 20 months ago by
Assa Yeroslaviz
★ 1.8k • written 2.3 years ago by
dariober
14k
7
votes
2
replies
3.9k
views
Tutorial:
How to extract fastq files from SRA data that contains both paired and unpaired reads
fastq-dump
sra
updated 13 months ago by
Ram
43k • written 8.1 years ago by
thomaskuilman
▴ 850
3
votes
2
replies
3.9k
views
Tutorial:
Galaxy Tutorial on ChIP-seq
galaxy
ChIP-Seq
updated 11 months ago by
Ram
43k • written 7.1 years ago by
anton
▴ 30
3
votes
1
reply
3.8k
views
Tutorial:
Importance of Array Quality Control - arrayQualityMetrics (PART I)
gene
R
updated 13 months ago by
Ram
43k • written 7.9 years ago by
majuang66
▴ 140
9
votes
14
replies
3.7k
views
6 follow
Tutorial:
Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 18 months ago by
Angelina_G
▴ 10 • written 2.2 years ago by
thehung92phuyen
▴ 40
10
votes
2
replies
3.7k
views
Tutorial:
Graph visualization with igraph in R
Visualization
igraph
Graph
R
Network
updated 11 months ago by
Ram
43k • written 7.1 years ago by
Jean-Karim Heriche
27k
1
vote
0
replies
3.7k
views
Tutorial:
embarrassingly easy parallel in Python, Perl and R
parallel
updated 21 months ago by
Ram
43k • written 8.5 years ago by
Echo
▴ 70
28
votes
0
replies
3.7k
views
Tutorial:
Building Docker images
singularity
docker
container
21 months ago by
ATpoint
82k
3
votes
0
replies
3.7k
views
Tutorial:
Sorting GFF/GTF files
gtf
gff
updated 14 months ago by
Ram
43k • written 3.8 years ago by
Juke34
8.6k
0
votes
0
replies
3.6k
views
Tutorial:
Park Test for Heteroskedasticity In R Commander
R
Park-Test
updated 11 months ago by
Ram
43k • written 6.3 years ago by
helgasaraswati
▴ 10
411 results • Page
4 of 9
Recent Votes
Answer: GRCh38.gmap file
Comment: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: Design matrix Differential expression analysis
A: PCA plot from read count matrix from RNA-Seq
A: PCA plot from read count matrix from RNA-Seq
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Comment: The GDC Legacy Archive is retiring soon.
by
Zhenyu Zhang
★ 1.2k
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…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Zhenyu Zhang
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These TCGA samples were taken 10 ~ 20 years ago, and there is no way they have been treated by the modern immunotherapy. Are you sure tha…
Comment: Design matrix Differential expression analysis
by
Gordon Smyth
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> When is it recommended to use the design <- cbind(Intercept=1,Group=c(-1,-1,-1,1,1,1)) It is not recommended. No such code appears anywh…
Comment: GRCh38.gmap file
by
lorena9132
▴ 10
Hi Mathew, The .txt files provided in the link differ from the .gmap files, but after several attempts, I succeeded in generating the .gma…
Answer: GRCh38.gmap file
by
Mathew
▴ 30
Hi, I have spent some time searching for a GRCH38 map file for you. I have found a certain publication that uses a hg38 genetic map file…
Answer: Association study using SNP data
by
Mathew
▴ 30
Hi, You asked three questions so I will attempt to help the best I can **What should be the optimal GC score cutoff** It sounds li…
Comment: Design matrix Differential expression analysis
by
SHN
▴ 40
Thank you for your explanation. I am working on the cell lines and I am investigating the effect of the treatment on the expression level, …
Answer: Issues with Mixture file when using CIBERSORTx
by
vjanve
• 0
I ran into same issue of "duplicated gene symbol(s)": 1: In CIBERSORTxFractions(sigmatrix = sigmatrix, mixture = mixture, : 22292 dup…
Comment: creating batch colum for batch correction
by
Expert
▴ 10
Thank you for your response. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are ind…
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by
ATpoint
82k
Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write dow…
Comment: Pindel Segmentation Fault Error
by
Ruqaiya
• 0
This the tool still problematic?
Comment: Segmentation error while using a tool
by
Ruqaiya
• 0
Thank you for the advice, i'll keep that in mind.
Comment: Segmentation error while using a tool
by
Ruqaiya
• 0
I am trying to reproduce some bioinformatics data from a research paper-[this paper][1] as i was asked to work on an MRSA bioinfo project, …
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Mensur Dlakic
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Most likely you didn't do anything wrong. Going by your previous post that you have only 8 GB of RAM, the most likely reason is the lack of…
Comment: Segmentation error while using a tool
by
Thanujay S
• 0
Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
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