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Landmark gene selection in L1000.
Connectivity Map: L1000 Platform and the First 1,000,000 Profiles. Subramanian A, Narayan R et al 1. I want to learn about the Affymetrix HGU133A microarray gene expression dataset that was exactly used when choosing
L1000 landmark-gene cmap
updated 17 days ago • kim
edgeR FDR always 1
DGEList(counts = cpm_data, group = group) y <- calcNormFactors(y) y <- estimateDisp(y) et <- exactTest(y) results_edgeR <- topTags(et) results_edgeR$table logFC logCPM PValue FDR hsa-miR-10395-3p 2.1245133 2.067156
FDR differential-gene-expression edgeR miRNA
updated 5 weeks ago • AngAdd
Creating a cytoscape bubble figure
Hi all, I'm interested in creating a figure similar to figure 4C-D in [Ganassi et al. 2022][1]: ![enter image description here][2] The text from the paper says the following: > Bubble plots demonstrating networks
cytoscape network GO
updated 5 weeks ago • Dave Carlson
How to install non-bioconda package in conda environment
Hi, I need to install GeneMark-ES/ET/EP in one of my conda environments and I was wondering how to to this. I would normally do "conda install .... " but this would not...Hi, I need to install GeneMark-ES/ET/EP in one of my conda environments and I was wondering how to to this. I would normally do "conda install .... " but this would not work
conda bioconda
updated 6 weeks ago • Diego
Best codeml model for estimating omega, M0 ?
What is the best codeml model to determine if a gene is undergoing positive, negative or neutral selection? At this point I am not interested in site specific omega values, but rather want to estimate a value for the whole gene. ete3 toolkit offers models from M0 all the way to M13. For the most part they seem to follow the same trend. I was wondering if M0...not interested in site specific omega…
codeml ete3 evol
updated 7 weeks ago • Adrian Pelin
Get metadat from the ICGC data portal
Hello all, I'm interested in exploring smoking-induced mutations. Therefore, I want to retrieve all the VCF files for lung cancer in smokers from the ICGC data portal. However, I'm not sure if the information regrading the smoking status is restricted since I can't find it but I know it exists (see *Alexandrov, Ludmil B., et al. "Mutational signatures associated with tobacco smoking i…
hg38 ICGC Cancer
updated 10 weeks ago • elisheva
Integrated Genome Browser (IGB) Office Hours
hours to answer any of your questions about IGB! Office hours will be on Tuesdays, 11:30AM-12:30PM ET, via this link: https://charlotte-edu.zoom.us/j/93684064365?pwd=Uy9WemJpcGNnNzZHWkt2WlgzOGt6UT09 (Meeting ID: 936 8406
Integrated-Genome-Browser IGB
updated 10 weeks ago • IGB Helper
Different relatedness estimates by PLINK and VCFTOOLS despite same method
the "--relatedness2" flag allows calculating relatedness statistics using the method by Manichaikul et al., BIOINFORMATICS 2010 (doi:10.1093/bioinformatics/btq559). That is, based on KING. According to the PLINK manual, PLINK uses
kinship vcftools PLINK relatedness
updated 3 months ago • 8armed
EMBL Course Hands-on course for sample preparation and data analysis in proteomics
perform an in-solution digest using Single-Pot Solid-Phase-enhanced Sample Preparation (SP3) (Hughes et al., Molecular Systems Biology, 2014) and tandem mass tag labelling (TMT). The SP3 technology was developed at EMBL. It enables
EMBLProteomics
updated 3 months ago • EMBL Events
Find Large-scale CNVs in whole exome sequencing
diazlab/CONICS/wiki/Tutorial---CONICSmat:-Inference-of-clones-in-GBM-single-cell-data-from-Darmanis-et-al
WES scRNA-seq CNV
updated 3 months ago • fifty_fifty
What are chromatin states ?
of genome-wide binding maps indicates that PcG and HP1 heterochromatin are nonoverlapping (de Wit et al., 2007). HP1 and PcG chromatin illustrate two important principles of chromatin organization: each type is marked by unique
genome ChIP-Seq
updated 3 months ago • rohitsatyam102
How to collapse leaves with the same name in ETE3 tree
I'm trying to collapse leaves that have the same name in ETE3's tree. I think I almost got it. Two leaves in my example (`A. thaliana`) have been combined into a single leaf, but not named. I would...like it to have the same name as its components. ```py from ete3 import Tree def collapsed_leaf(node): if len(node2labels[node]) == 1: return True else: return False t1 = Tre…
python ete3
updated 3 months ago • Andrzej Zielezinski
PCA plot interpretation (single population)
GWAS looking at hypertension (case/control) and have followed the QC tutorial from Marees et al., 2017. After pruning `--indep-pairwise 100 10 0.2` and `--maf 0.1`, I was left with 71139 variants to do PCA analysis. Most of the articles
PCA GWAS pruning
updated 3 months ago • Shane
Bulk RNA-seq: Batch correction in Bulk RNA-seq or microarray data
not only the product of biological processes: they are also the product of technical biases (Lander et al, 1999). ComBat is one of the most widely used tool for correcting those technical biases called batch effects. pyComBat...Behdenna et al, 2020) is a new Python implementation of ComBat (Johnson et al, 2007), a software widely used for the adjustment of batch effects
python RNA-seq batch-correction
updated 4 months ago • Julia Ma
Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-2
We suggest embedding the graph in two dimensions using UMAP (McInnes et al., 2018), see below. It is potentially more faithful to the global connectivity of the manifold than tSNE, i.e., it better preserves...the Leiden graph-clustering method (community detection based on optimizing modularity) by Traag et al. (2018). Note that Leiden clustering directly clusters the neighborhood graph of cells,…
scRNA-seq
updated 4 months ago • Julia Ma
Single-cell RNA-seq: Preprocessing: Data integration and batch correction-3
from benchmarking experiments including the single-cell integration benchmarking project [Luecken et al., 2021]. This project also produced a software package called [scib][12] that can be used to run a range of integration methods
scRNA-seq
updated 4 months ago • Julia Ma
Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-2
Ro/e) for each cluster in different tissues to quantify the tissue preference of each cluster (Guo et al., 2018; Zhang et al., 2018). The expected cell num- bers for each combination of cell clusters and tissues were obtained from
scRNA-seq SCSA
updated 4 months ago • Julia Ma
Single-cell RNA-seq: Preprocessing: Clustering space and evaluation
algorithm which outperformed other clustering methods for single-cell RNA-seq data analysis ([Du et al., 2018, Freytag et al., 2018, Weber and Robinson, 2016]). Since the Louvain algorithm is no longer maintained, using Leiden instead...is preferred. We, therefore, propose to use the Leiden algorithm[Traag et al., 2019] on single-cell k-nearest-neighbour (KNN) graphs to cluster single-cell datas…
scRNA-seq space clustering
updated 4 months ago • Julia Ma
Segementation fault when running rifdock
Hi! I followed the protocol provided by the paper: Cao,Longxing,et al."Design of protein-binding proteins from the target structure alone".Nature,vol.605,2022,pp.551-560,https://doi.org/10.1038
RIFDOCK
updated 5 months ago • anneday1998
Generating variant read count matrix, total read count matrix and binary/ternary mutaion matrix for SNV from scDNAseq FASTQ files
Leung et al., 2017][1] paper mentioned in [Fig 1][2] data processing for CRC patients was sequenced as single cell for both SNV (with MDA WGA
SNV mutationMatrix tumorPhylogeny scDNAseq mutaion
updated 5 months ago • supernovamik
Assistant Professor: Molecular Biology
genetics, and bioinformatics with applications ranging from image analysis for cryo-EM, cryo-ET, and advanced light microscopy to AI/ML-based modeling of protein structure-function- evolution as well as dynamic intracellular
Biology Molecular UCSD
updated 5 months ago • lta
Osmotic permeability of water transport in aquaporins
this channel . The protocol for calculation based on the collective diffusion model proposed by Zhu *et al*. I am not able to get how I can do this . Can Someone help me in this regard. Thanks
permeability Osmotic transport Water
updated 5 months ago • Peerzada
How can I amend the output of a DIAMOND python script?
that looks like so: 1.4435847095507564 125 COG0683 | E 1.4435847095507564 125 COG0834 | ET 1.3973899988451322 121 COG4663 | Q The first column is the percentage abundance for that particular COG. The second column...this: 1.4435847095507564 125 COG0683 | E AqS1v2_03414 1.4435847095507564 125 COG0834 | ET AqS1v2_05420 1.3973899988451322 121 COG4663 | Q…
Python Diamond COG_analysis
updated 5 months ago • eamaunders
bam or VCF files from GSE75010
Hi all I'm planning to run a variant calling analysis using Microarray data GSE75010 that contains GSE75010_RAW.tar and GSE75010_complete_dataset.csv.gz. I used to download the .fastq files using SRA Run numbers through Ubuntu/Linux to get .bam and VCF files. However, this is not the case as there are no SRA numbers. Someone can help me? Regards, Bony
bam file or VCF
updated 5 months ago • ahonya
The Biostar Herald for Monday, November 27, 2023
WGS data of over 1,000 individuals from the Northern Sweden Population Health Study (NSPHS) (Höglund et al. 2019). We called CNVs using CNVnator, and tested for association between CNVs and the variation in a large set of proteins
herald
updated 5 months ago • Biostar
Phylogenetic tree for my bins with abundance, genome size etc
I would like to create a tree for my MAGs/Bins like the image shown below. Can anyone please share me the steps/scripts in detail? When I used, gtdbtk de_novo_wf to analyze a set of bin files with -skip_gtdb_refs. I always ends up with the following error. *[2023-11-20 12:55:35] INFO: Read custom taxonomy for 45 genomes. [2023-11-20 12:55:35] INFO: Reassigned taxonomy for 45 GTDB represent…
Bins tree
updated 5 months ago • aswin
Uncovering the Genetic Basis of Rare and Complex Diseases through Whole Genome Sequencing (WGS)
over multiple years, and successfully coordinating genotypic and phenotypic information. Chen et al. developed PanSeer, a noninvasive blood test for cancer-specific methylation signatures from circulating tumor DNA...Longitudinal Study in which 123,511 healthy patients were followed for cancer occurrence. Chen et al. also developed a machine learning method (classifier) to classify samples as com…
genome WGS illumina GWAS sequence
updated 6 months ago • Novogene
Uncovering Potential Therapeutic Targets for Drug Development through Single Cell Sequencing Techniques
during ITP, including activation of immune states during most phases. In another example, Tang et al. used single-cell multi-omics technology to investigate MAIT (mucosal-associated invariant T) cell dysfunction in HIV...to become an increasingly important tool in the fight against diseases. **References** [1]. Ji P et al. In vivo multidimensional CRISPR screens identify Lgals2 as an immunother…
immunotherapy therapeutic-targets drug-development rnaseq single-cell-sequencing
updated 6 months ago • Novogene
Using Long-read Sequencing Technology to Explore the Complex Structure of Transcripts
The long-read sequencing technology (also known as third generation sequencing), which can directly obtain the full-length mRNA sequence and structural information without splicing is the foundation for the full-length transcriptome. It can offer valuable insights into a number of disease-related issues. This long-read sequencing technology has unparalleled advantages in the complex structural an…
Nanopore PacBio long-read-sequencing sequencing complex-structure
updated 6 months ago • Novogene
Options for assigning cell labels to barcodes from CITE-seq experiment
assign cell types to barcodes based on the ADT expression data. I recently read a paper by [Stuart et al., 2019][1] that describes a method for transferring this type of information to other datasets using canonical correlation
single-cell
updated 6 months ago • Chris Dean
Using easyPubMed and scholar package to get all citations of your paper
1:nrow(publications_top30), function(x) { pub <- publications_top30[x,] paste( gsub("\\.\\.\\.", "et al.",pub$author), pub$title, pub$journal, pub$number, pub$year, pub$doi, sep = ", " ) }) df<- ldply(pub_list_temp) write.table(df, file = "references.txt
scholar easyPubMed
updated 6 months ago • rohitsatyam102
Normalized data values very different from unnormalized counts in Seurat
I the sceasy R package to convert Burclaff et al.'s (2022) single-cell data (GSE185224) from scanpy H5AD data to a Seurat R object. My object's UMAP looks similar to the authors
scRNA Single-cell Seurat
updated 6 months ago • AHerik
vg call coverage/suppport
less coverage (and for single sample data, be less likely to be called)? I wasn't sure from Hickey et al. 2020 but apologies if I've missed this somewhere. Best wishes, Daniel Wood
vg
updated 7 months ago • Danny
Code for implementation of Network Component Analysis
programming language) code for Network Component Analysis, proposed in the following paper: Liao et al., (2003) "Network component analysis: Reconstruction of regulatory signals in biological systems", PNAS, 100 (26) I came across...Page not found" Network Component Analysis has been used in many other papers (for example: Ling et al., (2013) "Transcriptome response to alkane biofuels in Saccha…
matlab nca python network-component-analysis
updated 7 months ago • sayakm.biotech
Does ploidy in variant calling affect admixture detection with TreeMix?
to a classical phylogenetic approach. I want to take an approach similar to the study by [Fay et al. (2019)][1] however I have questions regarding the validity of using TreeMix on polyploid strains. Yeasts have various ploidy...are tetraploid, and therefore I made tetraploid variant calls. On the other hand, I can see that Fay et al. used `sample_ploidy=1` in their pipeline. The standard treemix …
ploidy admixture SNP TreeMix
updated 7 months ago • Michael
How to extend contigs from single-end reads?
Hi all, I have raw sequencing datas of metagenomes and all of them are single-end reads. I would want to prolong/extend contigs. I thought of PRICE (Ruby, JG., *et al*, 2013) but it only works with paired-end reads. Do you have any recommendation on what software could I use? Thank you for your...of them are single-end reads. I would want to prolong/extend contigs. I thought of PRICE (Ruby, JG…
contigs contig-extension
updated 7 months ago • A_heath
Which reference genome, DNA or cDNA and why?
Dear Community, The goal of my study is analyze Human RNA-seq and to take the gene count for RNA-seq and then apply the DESq2. I must use the most recent genome reference, but I am unsure of which FASTA file to use from Ensembl. DNA or cDNA and why? Best,
or DNA cDNA
updated 8 months ago • وفاء
Join Our Online Course: Incorporating Paleogenomes into Evolutionary Genomics Studies
you will engage in practical sessions and gain hands-on experience using data from the recent Kirch et al. study on ancient threespine sticklebacks. [1]: https://docs.google.com/forms/d/e/1FAIpQLSda3fRIgpo8ERDRjliF3bCU0lFiDC
Paleogenomics Genomics aDNA Adaptation-Genomics
updated 8 months ago • carlopecoraro2
Unsupervised clustering on gene expression data
discoveries. For more information on the methodology please refer to the seminal paper by [Monti et al. (2003)][4] and the `ConsensusClusterPlus` package [manual][5]. ```r #________________________# Clustering & Cluster assignment
gene-expression clustering RNA-seq
updated 9 months ago • Hamid Ghaedi
How to preprocess and visualize beautifully scRNA-seq with omicverse?
the neighborhood graph We suggest embedding the graph in two dimensions using UMAP (McInnes et al., 2018), see below. It is potentially more faithful to the global connectivity of the manifold than tSNE, i.e., it better preserves...the Leiden graph-clustering method (community detection based on optimizing modularity) by Traag *et al.* (2018). Note that Leiden clustering directly clusters the ne…
scRNA-seq seurat scanpy Python
updated 9 months ago • Starlitnightly
Highly degenerate primers and BLAST
Leray et al 2013][1]'s CO1 primers are commonly used in labs looking to detect vertebrates. I've been trying to include them in my in silico
blast
updated 9 months ago • Philipp Bayer
Kraken2 + Bracken with short reads (~20 bases) as input
but I would hope that I can do some analysis on this. I have done a trial run following the Lu et al. (2022), with the "Standard" database (third one down at [https://benlangmead.github.io/aws-indexes/k2][2]) using the Kraken2 and
Bracken smallRNAseq Kraken2
updated 9 months ago • jammydodger123456
Filter gene with low count in RNA-seq using a function from edgeR
r d <- DGEList(counts=counts,group=factor(conditions)) keep <- filterByExpr(d) bcv <- 0.2 et <- exactTest(keep, dispersion=bcv^2) Error in exactTest(d, dispersion = bcv2) : Currently only supports DGEList objects as the
edgeR RNA-seq
updated 9 months ago • Chris
How to read count information from an old RGB based Agilent DNA array
data to test a CNV filtration method I am working on. I would really like to use data from Conrad et al (2007), mostly because it is highly cited - and easy to access. Link here https://www.ebi.ac.uk/biostudies/arrayexpress/studies
CNV Agilent DNA WGS
updated 9 months ago • K.patel5
Postdoctoral Research Fellow position in neurodevelopmental genetics research
A substantial amount of data, and tools, already exist for these ongoing projects (e.g., Trost et al, 2020 *Nature* and Mojarad et al, 2021 *Transl Psychiatry*). The postdoctoral researcher will be able to jump straight into
R genome next-gen
updated 9 months ago • ryan.yuen
Phylogenetic tree visualization
be able to see how many XPA or other proteins are there for Intoshia linei. Can I do this with ete3? Or any other suggestions? Thanks in advance. [1]: /media/images/843bdb08-b956-4331-a2da-aa0bbd78
ete3 phylogenetics
updated 9 months ago • M.
How to draw density plots for multiple groups with annotation
Hello, I would like to draw a histogram with annotations like the one below. The figure is from Liu et al 2021 Genome Research (https://genome.cshlp.org/content/early/2021/12/28/gr.275453.121.full.pdf). Any pointers or package
visualization
updated 10 months ago • mikothebichon
Functional classification of genes
I want to create a heatmap just like this one : ![Heatmap] [1] Reference: Konstantinidis, Ioannis, et al. "Major gene expression changes and epigenetic remodelling in Nile tilapia muscle after just one generation of domestication
classification heatmap clustering
updated 10 months ago • G
Pathomx: Metabolic Pathway Visualisation And Analysis
do what I can. ### Citing pathomx If you use Pathomx in your analysis please cite: MA Fitzpatrick et al. [Pathomx: an interactive workflow-based tool for the analysis of metabolomic data][12] *BMC Bioinformatics* 2014 doi:10.1186
python pathway-visualization
updated 10 months ago • Martin Fitzpatrick
Lofreq: A Fast And Sensitive Variant-Caller For Inferring Single-Nucleotide Variants From Ngs Data
and 1.5 hours to run on a 100X coverage human exome data. --- The relevant publication is: [Wilm et al. (2012). LoFreq: A sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity
snp next-gen somatic-variant
updated 10 months ago • Andreas
963 results • Page 1 of 20
Recent Votes
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
Answer: Details on salmon index
Comment: zero TPM for many gene including housekeeping when using kallisto
Sequence Alignment from Scratch with BWA
Answer: mitochondrial genome assembly pipeline
Comment: Help! Reconstruction of locus, order contigs
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
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Scholar to Peter 6.0k
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Recent Replies
Comment: Help! Reconstruction of locus, order contigs by dthorbur ★ 2.0k
I don't understand your comment. What do you mean? > my idea is not to have to write it down If you have an alignment already, why can't…
Comment: Help! Reconstruction of locus, order contigs by GenoMax 142k
Please use `ADD REPLY/ADD COMMENT` when responding to existing content. `SUBMIT ANSWER` is for new answers to the original question.
Comment: Details on salmon index by Rob 6.6k
Hi Lorenzo, That is correct. The initial version of salmon used the RapMap index explained above. When we published the selective align…
Comment: Help! Reconstruction of locus, order contigs by BATMAN • 0
Thanks for your reply, my idea is not to have to write it down. What I have is an alignment of the .gbk from the progressiveMauve. It would…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
I did some digging aroumd, no static binary. Plus it seems you need to roll your own program.
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
We tested it, however, it does not seem to produce a fast a file of the results or anything that we can easily parse. It produces a CIGAR a…
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint yes but for example for the kallisto results I have expression for 2080 genes (transcripts) and the rest are 0 but in my STAR resu…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri by marco.barr ▴ 130
great team work! why can't you access and do the calculation for the other components too? can't you extract the information from the other…
Comment: zero TPM for many gene including housekeeping when using kallisto by ATpoint 82k
Yes, but this is what I am saying: GAPDH in human has at least 6 annotated transcripts. Have you looked at all of them? Maybe that particul…
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint these are from PBMC. no they are different genes. for example ENST00000229239.10 is GAPDH. in STAR I got a lot of reads aligned …
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@dariober: I have to use kallisto for our downstream pipeline.
Comment: zero TPM for many gene including housekeeping when using kallisto by ATpoint 82k
Which celltype is this? Are these transcripts of the same gene, and of which gene?
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint the question is updated. the first command shows how the index is built.
Comment: Help! Reconstruction of locus, order contigs by dthorbur ★ 2.0k
Is the *de novo* annotation required for each contig? Reconstructing homologous regions in many genomes can be tricky regardless, but is es…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri by diqixiaoyaoer ▴ 20
You can have a look on my answer. I have post it below.
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