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News: NCBI BLAST ClusteredNR database now available for blastx and PSI-BLAST searches
PSI-BLAST blastx BLAST NCBI ClusteredNR
11 weeks ago by PeterC_NCBI ▴ 210
1
vote
0
replies
770
views
News: New ebook: From cell line to Command line to learn computational biology
snakemake biology unix RNAseq computational
12 weeks ago by Ming Tommy Tang ★ 2.9k
0
votes
0
replies
359
views
News: Winter School in Bioinformatics - last seats available
Genomics Unix RNA-seq docker
updated 7 weeks ago by 38k • written 12 weeks ago by ★ 2.3k
0
votes
0
replies
240
views
News: Virtual RNA-seq Analysis (Model Organism) Workshop
virtual expression rna-seq analysis workshop
12 weeks ago by mia.nahom ▴ 10
0
votes
0
replies
276
views
News: Introduction to R Shiny course
WebApplications R RShiny
3 months ago by carlopecoraro2 ★ 2.3k
1
vote
0
replies
315
views
News: New version of ElasticBLAST (1.0.0) available.
NCBI ElasticBLAST BLAST
3 months ago by PeterC_NCBI ▴ 210
0
votes
1
reply
306
views
News: Courses in January - still a few seats available
R-Shiny Genomics Unix R
updated 7 weeks ago by 38k • written 3 months ago by ★ 2.3k
0
votes
0
replies
193
views
News: Sex Chromosome Evolution course
Genomics Sex-Chromosome-Evolution
updated 3 months ago by 38k • written 3 months ago by ★ 2.3k
0
votes
0
replies
240
views
News: Cellosaurus release 44 is available
cellosaurus cell-line
updated 3 months ago by 38k • written 3 months ago by ▴ 110
0
votes
0
replies
219
views
News: Introductory video to the Cellosaurus
cellosaurus cell-line
updated 3 months ago by 38k • written 3 months ago by ▴ 110
0
votes
3
replies
510
views
News: Nvidia Clara Parabricks is FREE for R&D
nvidia workflow gpu
updated 3 months ago by 2.6k • written 3 months ago by 153k
2
votes
3
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343
views
News: NCBI Comparative Genome Viewer now allows searches for genes across aligned assemblies
Browser NCBI Alignments Genome
3 months ago by PeterC_NCBI ▴ 210
1
vote
6
replies
687
views
News: Course - FLOW CYTOMETRY ANALYSIS WITH R/BIOCONDUCTOR
Bioconductor FlowCytometry R
updated 10 weeks ago by ▴ 70 • written 3 months ago by ★ 2.3k
0
votes
0
replies
187
views
News: INTRODUCTION TO ANALYTICAL PALEOBIOLOGY: FOSSIL RECORD BIASES, DIVERSITY, & BIOGEOGRAPHY
Biogeography Paleobiology R
3 months ago by carlopecoraro2 ★ 2.3k
1
vote
0
replies
200
views
News: Analysis of Cancer Genomes Using R and Bioinformatic Tools
Genomics Cancer-Genomics R
updated 3 months ago by 38k • written 3 months ago by ★ 2.3k
0
votes
0
replies
313
views
News: course - GENOME ASSEMBLY USING OXFORD NANOPORE SEQUENCING
Long-reads Assembly Nanopore Genome
3 months ago by carlopecoraro2 ★ 2.3k
0
votes
0
replies
171
views
News: Online training - VERSION CONTROL FOR RESEARCHERS
Version Control Git Github
3 months ago by carlopecoraro2 ★ 2.3k
0
votes
1
reply
242
views
News: Research Training In NGS Data Analysis
analysis data-analysis
updated 3 months ago by 38k • written 3 months ago by • 0
0
votes
0
replies
283
views
News: Bayesian regression modeling in R course
RegressionModeling Bayesian R
4 months ago by carlopecoraro2 ★ 2.3k
0
votes
4
replies
466
views
News: Ensembl Release 104 and newer GTF files no longer have genes sorted by position
Ensembl GTF
updated 3 months ago by ★ 2.2k • written 4 months ago by ▴ 10
0
votes
0
replies
227
views
News: Genome Assembly and Annotation course
Annotation Nanopore GenomeAssembly Pacbio
4 months ago by carlopecoraro2 ★ 2.3k
3
votes
0
replies
961
views
News: Changes to the default NCBI BLAST nucleotide database (nt). Learn more and provide feedback!
NCBI Databases BLAST
4 months ago by PeterC_NCBI ▴ 210
0
votes
0
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235
views
News: Nextflow online training
Nextflow Workflow Reproducibility
updated 3 months ago by 38k • written 4 months ago by ★ 2.3k
0
votes
2
replies
953
views
News: :: FINAL CALL :: Next-Generation Sequencing Data Analysis: A Practical Introduction (December 12-14, 2022 in Munich, Germany)
rnaseq dnaseq sequencing ngs workshop
4 months ago by David Langenberger 9.9k
0
votes
0
replies
267
views
News: The Association for Single Cell Analysis (ASCA)
genomics singlecell metabolomics sequencing proteomics
4 months ago by dnsv.ev • 0
0
votes
0
replies
221
views
News: Deep Learning in Population Genomics and Phylogeography
DeepLearning Phylogeography PopulationGenomics
4 months ago by carlopecoraro2 ★ 2.3k
0
votes
0
replies
232
views
News: Metabarcoding in Microbial Ecology Workshop
Qiime2 R Metabarcoding Microbial-Ecology
4 months ago by carlopecoraro2 ★ 2.3k
1
vote
2
replies
357
views
News: Gene Set Enrichment Analysis in R/Bioconductor
Gene-Set-Enrichment-Analysis R Cancer-Genomics GSEA
4 months ago by carlopecoraro2 ★ 2.3k
0
votes
0
replies
230
views
News: Analysis of RNA sequencing data with R/Bioconductor course.
Bioconductor RNAseq R
4 months ago by carlopecoraro2 ★ 2.3k
0
votes
0
replies
334
views
News: Winter School in Bioinformatics
course workshop
updated 3 months ago by 38k • written 4 months ago by ★ 2.3k
1
vote
0
replies
303
views
News: Introduction to Nextflow
Nextflow
updated 3 months ago by 38k • written 4 months ago by ★ 2.3k
0
votes
2
replies
456
views
News: Seascape Genomics in R
Genomics Seascape R
updated 3 months ago by 38k • written 5 months ago by ★ 2.3k
0
votes
0
replies
225
views
News: Bioinformatics courses in November
Bioconductor Genomics R
updated 3 months ago by 38k • written 5 months ago by ★ 2.3k
0
votes
0
replies
305
views
News: Flow cytometry analysis with R/Bioconductor course
Bioconductor R Cytometry Flow
5 months ago by carlopecoraro2 ★ 2.3k
0
votes
0
replies
227
views
News: course: RNA-seq analyses in non-model organisms
differential Bioconductor RNAseq expression non-model organisms analysis R
5 months ago by carlopecoraro2 ★ 2.3k
0
votes
0
replies
252
views
News: course - Developing R/Bioconductor packages for genomics
developing package Bioconductor Genomics R
5 months ago by carlopecoraro2 ★ 2.3k
2
votes
0
replies
267
views
News: Four NCBI workshops in October (BLAST, Primer-BLAST, Metagenome analysis, Structures in iCn3D)
metagenomics MagicBLAST BLAST NCBI Primer-BLAST
5 months ago by PeterC_NCBI ▴ 210
0
votes
0
replies
329
views
News: course - Unix and shell scripting for bioinformatics
bash Shell-scripting Unix
updated 3 months ago by 38k • written 5 months ago by ★ 2.3k
0
votes
0
replies
278
views
News: course: Data Visualization in Python
Visualisation Python Data
updated 5 months ago by 127k • written 5 months ago by ★ 2.3k
0
votes
0
replies
259
views
News: Seascape Genomics in R course
Genomics R Seascape Population
6 months ago by carlopecoraro2 ★ 2.3k
0
votes
0
replies
275
views
News: Cellosaurus API
line cell API
6 months ago by Amos Bairoch ▴ 110
0
votes
0
replies
274
views
News: Cellosaurus release 43 is available
cellosaurus cell-line
updated 3 months ago by 38k • written 6 months ago by ▴ 110
0
votes
0
replies
231
views
News: Genomics Webinar: Using Mastermind’s New ClinVar Integration to Accelerate Clinical Diagnoses
variant-interpretation genomics database webinar
updated 3 months ago by 38k • written 6 months ago by • 0
0
votes
0
replies
212
views
News: course: Population Genomic Inference from Low-coverage Whole-genome Sequencing Data
whole-genome genomics population low-coverage sequencing
updated 6 months ago by 21k • written 6 months ago by ★ 2.3k
0
votes
0
replies
219
views
News: :: FINAL CALL :: RNA-Seq Data Analysis Workshop (October 25 - 28, 2022 in Leipzig, Germany) - 2 seats left
RNA-Seq workshop transcriptomics
6 months ago by David Langenberger 9.9k
0
votes
0
replies
204
views
News: Getting the most out of R course - last call
ggplot2 R tidyverse
6 months ago by carlopecoraro2 ★ 2.3k
0
votes
0
replies
277
views
News: The NCTR Indel Calling from Oncopanel Sequencing Data Challenge Winners have been announced!
FDA-challenge
updated 3 months ago by 38k • written 6 months ago by ▴ 10
1
vote
0
replies
245
views
News: Webinar (free) on Multimodal Single-Cell Data from winner of NeurIPS 2021
ATAC-seq CITE-seq scRNA-seq
6 months ago by Alexander ▴ 70
1
vote
0
replies
253
views
News: course Reproducible Analysis With R
R Reproducibility analysis Data
6 months ago by carlopecoraro2 ★ 2.3k
0
votes
0
replies
277
views
News: Virtual Genome Assembly workshop
Genome Workshop assembly Virtual
6 months ago by singh.vijender ▴ 70
1,000 results • Page 2 of 20
Recent Votes
Answer: multiallelic variants
Answer: LIMMA calculates identical adj.P.Val for different proteins from proteomics
Comment: Hard clip fastq
Answer: Hard clip fastq
Answer: Hard clip fastq
Answer: Hard clip fastq
Comment: Protein name in GenBank
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Answer: MapSplice2 gives error if the thread count (-p value) is greater than 2 by vishal.koparde ▴ 10
Any updates??
Comment: how to know what adapter sequences to trim for RNA-seq? by lunarskye222 • 0
Do you happen to know if the middle part of this udi barcode (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCTACATATCTCG) is also part of the TruSeq a…
Comment: Hard clip fastq by GenoMax 127k
If you simply want the reads to be compatible in length then do not adapter trim.
Comment: Hard clip fastq by samuel ▴ 180
@ATpoint, so no adapter trimming first? Just trim the raw fastq?
Answer: Confused on strandedness, what are antisense transcripts? by dsull ★ 4.0k
RNA pol always transcribes 5' -> 3'. This has nothing to do with +/-. Think of it on the DNA level: If the mRNA made is the same sequenc…
Comment: Protein name in GenBank by GenoMax 127k
If you must do this programmatically then collect all cases where things differ in order of words (or number of words) like the example abo…
Answer: Hard clip fastq by GenoMax 127k
You can also use `reformat.sh` from [**BBMap suite**][1] as follows reformat.sh -Xmx2g in1=R1.fq.gz in2=R2.fq.gz out1=R1_trim.fq.gz …
Answer: Hard clip fastq by ATpoint 70k
Use `seqtk trimfq`. It makes sense to trim first to your desired length and then run identical downstream processing for a fair comparison.…
Comment: Protein name in GenBank by Mensur Dlakic ★ 23k
I think you either take time to do it properly, or you will end up missing some proteins. BLAST sequence search, even on 1500 genomes, can …
Comment: Log2 FC Threshold by ATpoint 70k
Since OP is using GEO2R which uses limma the appropriate function (need to run manually, GEO2R does not support) is `limma::treat()` rather…
Answer: Adding median value to VlnPlot in Seurat by Ming Tommy Tang ★ 2.9k
If you know ggplot2, you can `get_expression_data` function in here https://divingintogeneticsandgenomics.rbind.io/post/how-to-do-gene-corr…
Answer: how to know what adapter sequences to trim for RNA-seq? by Ming Tommy Tang ★ 2.9k
You may use fastp which detect adaptors by itself https://github.com/OpenGene/fastp#adapters
Answer: Variant Calling with Multiple Individuals in Freebayes by Ming Tommy Tang ★ 2.9k
It looks like you can provide multiple bam files and output a gVCF file https://github.com/freebayes/freebayes#usage
Answer: Log2 FC Threshold by Ming Tommy Tang ★ 2.9k
This is hard to say. Some genes could play a very different role, even with little change. You want to focus on the large FC genes initiall…
Answer: Log2 FC Threshold by Mensur Dlakic ★ 23k
There is no prescribed logFC that everyone follows. The point is to convince yourself and others - those reviewing your papers and grants -…
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