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409 results • Page 4 of 9
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12
votes
1
reply
5.0k
views
Tutorial: RepSeq data processing and analysis
immunology tcr repseq sequencing repertoire
updated 18 months ago by 43k • written 8.7 years ago by 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 43k • written 8.2 years ago by ★ 4.3k
11
votes
3
replies
1.4k
views
Tutorial: Creating great documentation for bioinformatics software
Software-Documentation
updated 12 months ago by 43k • written 7.8 years ago by 7.1k
11
votes
7
replies
14k
views
Tutorial: Removing rows with duplicate values based on 1 or more key values - linux awk
awk linux bash
updated 11 months ago by 43k • written 6.6 years ago by 87k
11
votes
7
replies
11k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 11 months ago by 43k • written 3.1 years ago by ▴ 410
11
votes
7
replies
2.2k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
12 months ago by barslmn ★ 2.1k
11
votes
1
reply
2.6k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 13 months ago by 43k • written 3.3 years ago by ★ 27k
11
votes
0
replies
6.8k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 13 months ago by 43k • written 3.3 years ago by 141k
10
votes
3
replies
4.5k
views
Tutorial: Video: Alternative Splicing and Primer Design
RNA-Seq IGB
updated 15 months ago by 43k • written 9.6 years ago by ▴ 860
10
votes
31
replies
11k
views
10 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 5 months ago by • 0 • written 6.3 years ago by ▴ 320
10
votes
2
replies
3.7k
views
Tutorial: Graph visualization with igraph in R
Visualization igraph Graph R Network
updated 11 months ago by 43k • written 7.0 years ago by 27k
10
votes
6
replies
4.1k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 22 days ago by 43k • written 6.2 years ago by 87k
10
votes
2
replies
3.5k
views
Tutorial: How to find PubMed records where you were author (member) as part of a consortium
pubmed
updated 20 months ago by 43k • written 8.4 years ago by 20k
10
votes
0
replies
2.6k
views
Tutorial: Introduction to Next Generation Sequencing (Part 1)
polony emulsion-pcr next-gen-sequencing
updated 18 months ago by 43k • written 8.7 years ago by ▴ 100
10
votes
5
replies
23k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 13 months ago by 43k • written 5.7 years ago by ★ 9.4k
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 43k • written 3.3 years ago by 141k
10
votes
1
reply
2.3k
views
Tutorial: introduce a tool for fast identification of SARS-CoV-2 and other microbes from sequencing data
SARS-CoV-2 fastv COVID-19
updated 13 months ago by 43k • written 4.0 years ago by ★ 2.5k
10
votes
1
reply
9.2k
views
Tutorial: How to select reads with specific flag using samtools
next-gen-sequencing
updated 11 months ago by 43k • written 6.6 years ago by ▴ 110
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 43k • written 4.8 years ago by 6.3k
9
votes
0
replies
8.7k
views
Tutorial: Installing And Running Ncbi Blast
blast
updated 14 months ago by 43k • written 12.0 years ago by ▴ 540
9
votes
0
replies
3.6k
views
Tutorial: Video: Intro to All New Features in IGB 8.2
R paired-end IGB
updated 2.1 years ago by 43k • written 9.4 years ago by ▴ 860
9
votes
14
replies
3.7k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 17 months ago by ▴ 10 • written 2.1 years ago by ▴ 40
9
votes
0
replies
4.4k
views
Tutorial: Analysis of dbGaP data on the cloud
AWS dbGaP Cloud
updated 21 months ago by 43k • written 8.2 years ago by 19k
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 43k • written 6.8 years ago by 100k
9
votes
2
replies
5.5k
views
Tutorial: From Data import to Normalization in Microarray Analysis using in R (Part I)
gene R
updated 12 months ago by 43k • written 7.9 years ago by ▴ 140
9
votes
4
replies
5.4k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
8 months 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 43k • written 11.7 years ago by 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 43k • written 6.6 years ago by 87k
8
votes
19
replies
13k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
mysql orthomcl
updated 13 months ago by 43k • written 9.4 years ago by ▴ 600
8
votes
7
replies
8.3k
views
Tutorial: Getting Cegma/Genewise To Work On Centos, Rhel
centos genewise rhel cegma
updated 2.2 years ago by 43k • written 10.4 years ago by ★ 2.6k
8
votes
0
replies
2.7k
views
Tutorial: Pipes in R: An introduction and some advanced tips and tricks.
R
3.1 years ago by rpolicastro 13k
8
votes
17
replies
3.1k
views
Tutorial: Simple approach to RNA-seq (T-Bioinfo platform)
alignment next-gen-sequencing RNA-seq
updated 19 months ago by 43k • written 8.5 years ago by ▴ 340
8
votes
9
replies
11k
views
Tutorial: Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs (ONE-LINERS)
fastq fasta
updated 13 months ago by 43k • written 10.0 years ago by ★ 1.8k
8
votes
1
reply
1.4k
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
fasta awk
updated 13 months ago by 43k • written 3.1 years ago by 87k
8
votes
3
replies
2.8k
views
Tutorial: Free online interactive Ensembl training
ensembl training genome
updated 21 months ago by 43k • written 8.2 years ago by 23k
8
votes
2
replies
1.1k
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 8 months ago by 43k • written 8 months ago by ★ 2.5k
8
votes
1
reply
1.9k
views
Tutorial: A Guide to DNA Sequencing Techniques Part 1
dna sanger sequencing pyrosequencing
updated 13 months ago by 43k • written 8.8 years ago by ▴ 430
8
votes
2
replies
6.6k
views
Tutorial: Troubleshooting issues with SURPI pipeline for pathogen identification from complex metagenomic NGS data.
metagenomics clinical-genomics
updated 2.2 years ago by 43k • written 9.5 years ago by 12k
8
votes
12
replies
6.7k
views
Tutorial: Create your own VPN to access work resources from home
tinyproxy OpenVPN VPN
updated 12 months ago by 43k • written 7.9 years ago by 13k
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 12 months ago by 43k • written 7.9 years ago by ★ 5.1k
7
votes
2
replies
1.7k
views
Tutorial: A tale of two heatmap function
clustering heatmap
updated 12 months ago by 43k • written 7.6 years ago by ★ 3.9k
7
votes
2
replies
11k
views
Tutorial: Howto use NCBI programs behind a HTTP proxy
blast-plus HTTP-proxy SRA-toolkit
updated 21 months ago by 43k • written 8.2 years ago by ★ 1.8k
7
votes
2
replies
1.9k
views
Tutorial: Introduction to Human Genomics for Clinical Informaticists
genome
updated 11 months ago by 43k • written 6.7 years ago by ▴ 90
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 16 months ago by 43k • written 8.8 years ago by ★ 2.3k
7
votes
0
replies
5.3k
views
Tutorial: Mothur Analyzing 16S Of Ngs High Through-Put Sequencing
next-gen
updated 14 months ago by 43k • written 11.9 years ago by ▴ 120
7
votes
1
reply
2.2k
views
Tutorial: A gentle introduction to biogo
sequence golang biogo
updated 11 months ago by 43k • written 6.5 years ago by ★ 1.7k
7
votes
13
replies
13k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 10 months ago by 43k • written 5.2 years ago by ▴ 170
7
votes
0
replies
586
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
8 months ago by barslmn ★ 2.1k
7
votes
2
replies
3.5k
views
Tutorial: List Of Tools For Mapping High-Throughput Sequencing Data (2012)
next-gen mapping
updated 14 months ago by 43k • written 11.5 years ago by 11k
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 12 months ago by 43k • written 8.0 years ago by ▴ 850
409 results • Page 4 of 9
Recent Votes
Answer: Bedtools nuc : calculating the GC content in a sliding window
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
Comment: Questions about a bug when transferring cram file to bam file
A: Out Of Disk Space With Picard Tools ?
Exporting WGCNA step-to-step network construction objects into igraph object
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Recent Replies
Comment: Downloaded pdb's on rcsb.org by GenoMax 141k
For a non-programmer using the search builder link included above may be the best option. Even that is not very user friendly.
Comment: Downloaded pdb's on rcsb.org by Ram 43k
That's how they seem to have written their query - automating that is a bit of a pain though as it takes a crazy JSON as input.
Comment: Downloaded pdb's on rcsb.org by GenoMax 141k
You can use the "Advanced query" builder (https://www.rcsb.org/search/advanced ) to create a query like: https://www.rcsb.org/search?requ…
Comment: Downloaded pdb's on rcsb.org by Ram 43k
PDB has a search API: https://search.rcsb.org/#search-example-1 Here's the JSON from your search query: ``` { "query": { "type": "grou…
Comment: Downloaded pdb's on rcsb.org by iamsmor • 0
Thank you very much. Actually I looked at there, but actually I want to find something like according to search url like this [QUERY: Gene …
Comment: DEG analysis of RNA-seq data across multiple tissues and two conditions by BioinfGuru ★ 1.7k
great guidance ... thank you
Comment: error in CPC2 by Ram 43k
Ashok, what is CPC2? Please edit your post and add as much context as you can.
Comment: python file for cpc2 by Ram 43k
Ashok - someone else had to (guess and) add context to your post. Please give us as much information as you can in the first place - we can…
Comment: python file for cpc2 by Pierre Lindenbaum 161k
https://academic.oup.com/nar/article/45/W1/W12/3831091 > CPC2: a fast and accurate coding potential calculator based on sequence intrinsic…
Comment: error in CPC2 by GenoMax 141k
Looks like you are running code that was written for `python v.2.x` but you probably have `python v.3.x` or a newer version than `python v.…
Comment: Per base sequence content failed miserably by GenoMax 141k
If this is 16S sequencing just follow the standard workflows like Qiime2.https://docs.qiime2.org/2024.2/tutorials/overview/
Comment: Out Of Disk Space With Picard Tools ? by kjngo • 0
Thanks changing the tmp dir fixed the out of disk space error for me as well.
Answer: Downloaded pdb's on rcsb.org by GenoMax 141k
Download services for PDB are described on this page: https://www.rcsb.org/docs/programmatic-access/file-download-services It could be as …
Answer: How to compare the quality of assemblies by shelkmike ★ 1.2k
Since BUSCO results are almost identical but the assembly sizes differ significantly, I suppose that the difference between the assemblies …
Comment: differential gene expression analysis when not all samples have an untreated cou by nhaus ▴ 300
Thank you very much for your answer, that was very helpful! > Impossible to say. It depends on your data, particularly on how the donors …
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