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411 results • Page
3 of 9
Sort: replies
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Votes
Replies
39
votes
6
replies
19k
views
Tutorial:
Creating chromosome karyotype plot with R and ggplot2
ggplot2
R
chromosome
karyotype
updated 11 months ago by
Ram
43k • written 6.7 years ago by
steve
★ 3.5k
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
106
votes
6
replies
26k
views
6 follow
Tutorial:
Creating workflows with snakemake and conda
workflow
snakemake
conda
updated 13 months ago by
Ram
43k • written 5.6 years ago by
finswimmer
16k
67
votes
6
replies
26k
views
7 follow
Tutorial:
Rna-Seq Review Papers
RNA-seq
papers
updated 14 months ago by
Ram
43k • written 11.7 years ago by
Istvan Albert
100k
13
votes
6
replies
6.0k
views
Tutorial:
Trim & align paired-end reads in a single pass
align
trim
fastq
pipe
paired-end
updated 12 months ago by
Ram
43k • written 7.9 years ago by
dariober
14k
43
votes
6
replies
12k
views
Tutorial:
Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl
maf
tcga
vcf
updated 14 months ago by
Ram
43k • written 10.2 years ago by
Cyriac Kandoth
6.0k
44
votes
6
replies
24k
views
Tutorial:
Greatly speed up conda by using mamba
software
updated 2.3 years ago by
cameron.cowan
▴ 40 • written 3.1 years ago by
rpolicastro
13k
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
37
votes
5
replies
6.1k
views
Tutorial:
[Beginner] Introduction to bioinformatics file types
fastq
fasta
bed
SAM
updated 7 months ago by
gallardodiazmiriam
▴ 20 • written 8.8 years ago by
Luke Crichton
▴ 430
5
votes
5
replies
6.9k
views
Tutorial:
use firehose_get to download TCGA data
tcga
RNA-Seq
updated 11 months ago by
Ram
43k • written 6.5 years ago by
jmzeng1314
▴ 130
16
votes
5
replies
9.0k
views
Tutorial:
Using The Biomart Perl Api For Simple Queries
api
perl
biomart
updated 14 months ago by
Ram
43k • written 11.6 years ago by
Obi Griffith
20k
2
votes
5
replies
2.2k
views
Tutorial:
Building OMA database on SGE
oma
updated 12 months ago by
Ram
43k • written 7.8 years ago by
javier.herrero
▴ 10
29
votes
5
replies
6.4k
views
Tutorial:
Gnu Parallel Tutorial
parallel
gnu-parallel
updated 14 months ago by
Ram
43k • written 10.6 years ago by
ole.tange
★ 4.4k
21
votes
5
replies
6.8k
views
Tutorial:
Analysis of single-cell RNA-seq data
single-cell
RNA-Seq
updated 12 months ago by
Ram
43k • written 7.8 years ago by
Geparada
★ 1.5k
64
votes
5
replies
7.3k
views
10 follow
Tutorial:
Informatics of RNA-Seq.
next-gen
RNA-Seq
updated 18 months ago by
Ram
43k • written 8.7 years ago by
GouthamAtla
12k
15
votes
5
replies
15k
views
Tutorial:
How to create a mutation lolliplot with GenVisR
bioconductor
graphics
R
genvisr
updated 12 months ago by
Ram
43k • written 7.9 years ago by
Obi Griffith
20k
1
vote
5
replies
610
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq
TOSICA
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
10
votes
5
replies
23k
views
Tutorial:
Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 13 months ago by
Ram
43k • written 5.8 years ago by
Shicheng Guo
★ 9.4k
12
votes
5
replies
2.4k
views
Tutorial:
FASTA file split
fasta
updated 13 months ago by
Ram
43k • written 3.9 years ago by
Juke34
8.5k
54
votes
5
replies
15k
views
6 follow
Tutorial:
Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
r
updated 19 months ago by
Ram
43k • written 10.4 years ago by
Nicholas Spies
★ 1.2k
16
votes
5
replies
13k
views
6 follow
Tutorial:
Easy way to do GO enrichment in R
enrichr
RNA-Seq
gene
R
updated 13 months ago by
Ram
43k • written 6.4 years ago by
ahmad mousavi
▴ 800
70
votes
5
replies
11k
views
8 follow
Tutorial:
Bioinformatics For Metagenomic Analyses
QC
taxonomy
metagenomics
updated 2.1 years ago by
Ram
43k • written 10.1 years ago by
umer.zeeshan.ijaz
★ 1.8k
12
votes
5
replies
8.4k
views
Tutorial:
How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 12 months ago by
Ram
43k • written 7.9 years ago by
Shicheng Guo
★ 9.4k
9
votes
5
replies
2.3k
views
Tutorial:
What is new in samtools release 1.5 [Solstice Release] (21st June 2017)
samtools
updated 11 months ago by
Ram
43k • written 6.8 years ago by
Istvan Albert
100k
3
votes
4
replies
3.6k
views
Tutorial:
Gene Set Enrichment Analysis on T-BioInfo
gene
RNA-Seq
updated 11 months ago by
Ram
43k • written 5.5 years ago by
elia.brodsky
▴ 340
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 3.7 years ago by
Thind amarinder
▴ 340
9
votes
4
replies
5.5k
views
Tutorial:
Unsupervised clustering on gene expression data
gene-expression
clustering
RNA-seq
8 months ago by
Hamid Ghaedi
3.2k
12
votes
4
replies
5.4k
views
Tutorial:
*FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux
R
updated 14 months ago by
Ram
43k • written 3.2 years ago by
garden_giessen
▴ 130
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
24
votes
4
replies
7.7k
views
Tutorial:
Using EnrichedHeatmap for visualization of NGS experiments
heatmap
chip-seq
atac-seq
EnrichedHeatmap
updated 13 months ago by
Ram
43k • written 4.7 years ago by
ATpoint
82k
1
vote
4
replies
3.5k
views
Tutorial:
How to install C++ compilers/make from GNU for Gromacs?
Gromacs
Cpp-compilers
GNU
updated 12 months ago by
Ram
43k • written 7.9 years ago by
Hassan Rasouli
▴ 10
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
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
Ram
43k • written 11.1 years ago by
Sukhi Singh
11k
20
votes
4
replies
14k
views
Tutorial:
How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor
affymetrix
updated 14 months ago by
Ram
43k • written 11.1 years ago by
Obi Griffith
20k
32
votes
4
replies
7.9k
views
Tutorial:
Fast LD computation from VCF files using tomahawk
ld
snp
vcf
vcftools
bcftools
updated 13 months ago by
Ram
43k • written 5.5 years ago by
firestar
★ 1.6k
0
votes
4
replies
726
views
Tutorial:
Reverse pharmacology: how to predict drugs with genes or disease names?
drugs
drug-targets
genes
5 months ago by
Coremine Medical
▴ 20
1
vote
4
replies
3.4k
views
Tutorial:
Applying machine learning to NGS transcriptomic data
next-gen
RNA-Seq
updated 11 months ago by
Ram
43k • written 6.0 years ago by
elia.brodsky
▴ 340
12
votes
4
replies
2.2k
views
Tutorial:
Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR
DESeq2
updated 13 months ago by
Ram
43k • written 6.6 years ago by
KVC_bioinfo
▴ 590
20
votes
4
replies
8.6k
views
Tutorial:
DE analysis by edgeR
RNA-Seq
R
edgeR
updated 12 months ago by
Ram
43k • written 7.6 years ago by
zizigolu
★ 4.3k
19
votes
4
replies
8.9k
views
Tutorial:
Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 14 months ago by
Ram
43k • written 11.1 years ago by
Istvan Albert
100k
10
votes
4
replies
11k
views
Tutorial:
Using the MinION MinKNOW software on Ubuntu 1604
long-reads
oxford-nanopore
minion
updated 13 months ago by
Ram
43k • written 4.8 years ago by
colindaven
6.4k
20
votes
4
replies
2.6k
views
Tutorial:
Bash One-liners collection on Github
bash
linux
shell
updated 13 months ago by
Ram
43k • written 5.0 years ago by
nim.1111.ou
▴ 180
16
votes
3
replies
4.7k
views
Tutorial:
NCBI blast tutorial
ncbi
blast
updated 12 months ago by
Ram
43k • written 8.0 years ago by
Eric Normandeau
11k
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
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
3
votes
3
replies
1.1k
views
Tutorial:
multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation
RNAseq
multiomics
updated 3 months ago by
sil_bioinfo
▴ 40 • written 8 months ago by
Ming Tommy Tang
★ 3.9k
8
votes
3
replies
2.8k
views
Tutorial:
Free online interactive Ensembl training
ensembl
training
genome
updated 21 months ago by
Ram
43k • written 8.2 years ago by
Emily
23k
7
votes
3
replies
2.5k
views
Tutorial:
Automated dbSNP lookup by rsID position, plus genome build liftover
rsid
hg19
liftover
hg38
dbsnp
updated 12 months ago by
Randy H
▴ 110 • written 20 months ago by
Kevin Blighe
87k
7
votes
3
replies
2.8k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 7 days ago by
colindaven
6.4k • written 15 months ago by
Dr.Animo
▴ 130
11
votes
3
replies
1.4k
views
Tutorial:
Creating great documentation for bioinformatics software
Software-Documentation
updated 12 months ago by
Ram
43k • written 7.8 years ago by
venu
7.1k
411 results • Page
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Comment: what is the purpose of indexing the reference genome (Kallisto)
Answer: what is the purpose of indexing the reference genome (Kallisto)
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
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Comment: what is the purpose of indexing the reference genome (Kallisto)
by
i.sudbery
19k
Specifically: If we want to look up all the places where a 31mer is in a genome without and index, we have to compare that 31 to the first…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
benformatics
3.9k
This is way easier to do solely in R now 10 years later. library(GenomicFeatures) library(rtracklayer) ## import GTF…
Answer: what is the purpose of indexing the reference genome (Kallisto)
by
dsull
★ 5.8k
I'll see if I can explain things in super simple terms (albeit with some abuse of the actual technical details) to provide a conceptual und…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
Jalil Sharif
▴ 80
The updated code in R using rtracklayer for reading a gtf file. https://github.com/jalilsharif/gtf_utr_fix_r/blob/main/gencode_utr_fix_d…
Answer: Rare Disease Variant Pathway Analysis
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The_PyPanda
▴ 10
Thank you LauferVA, Your advice has been useful and I now a lot to think about and read. Also, I just wanted to clarify I do not ha…
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by
Antonio R. Franco
★ 5.1k
You cannot do it with Kallisto either. In fact, the indexation will fail in attempting to index a genome file
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by
ATpoint
82k
What is your question? Add details and clarity. Ask a precise question and please avoid opening more questions on the same underlying issue…
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by
Joe
21k
If you have the accession numbers can you not use something like `eutils`?
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Pierre Lindenbaum
161k
> Next, I tried using bedtools window but in your original post you said > tried finding the intersection of these bed files using bedto…
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Lada
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Thank you very much! I tried it out! This is a handy tool useful for many different applications, and in regards to my problem - although …
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
Thank you for replying Pierre. I first added a third column to the SNP bed file, so that I would get a range of 1 for each SNP awk 'B…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
> using bcftools Show us what you tried
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22k
> Hi, guys, there is a question about the genomic gVCF file. I wonder > that since gVCF contains the non-var block records, why after merge…
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Thank you for replying here; this helped me figure out why MAPK10 was missing from my results. It was also marked as a pseudogene in the En…
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Sofia
• 0
These are the first lines of the output: (Please is it normal to have NA in the P value column ?) CHR …
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